{ "bcoid": "GLY_000774", "title": "Yeast Protein Site Annotation", "description": "The Yeast Protein Site Annotation (UniProtKB) dataset contains yeast [taxid:559292] site annotations ...", "filename": "yeast_protein_site_annotation_uniprotkb.csv", "filetype": "csv", "categories": { "species": [ "Saccharomyces cerevisiae S288C" ], "molecule": [ "Protein" ], "tag": [ "site annotation" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P39979-1...", "HPA3..." ], [ "P39979-1...", "HPA3..." ] ], "headers": [ "uniprotkb_ca...", "gene_symbol..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "gene_symbol" }, { "type": "string", "label": "ann_type" }, { "type": "string", "label": "start_pos" }, { "type": "string", "label": "end_pos" }, { "type": "string", "label": "annotation" }, { "type": "string", "label": "ecoid" }, { "type": "string", "label": "ref_aa" }, { "type": "string", "label": "alt_aa" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" } ], [ "P39979-1", "HPA3", "Site_Annotation", "144", "144", "Important for catalytic activity", "ECO_0000250", "Y", "", "protein_xref_uniprotkb", "P39979" ], [ "P39979-1", "HPA3", "Site_Annotation", "144", "144", "Important for catalytic activity", "ECO_0000250", "Y", "", "protein_xref_pubmed", "Q06592" ], [ "P39979-1", "HPA3", "Modified_Residue_Annotation", "2", "2", "N-acetylserine", "ECO_0007744", "S", "", "protein_xref_uniprotkb", "P39979" ], [ "P39979-1", "HPA3", "Modified_Residue_Annotation", "2", "2", "N-acetylserine", "ECO_0007744", "S", "", "protein_xref_pubmed", "22814378" ], [ "Q07959-1", "IZH3", "Glycosylation_Annotation", "45", "45", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q07959" ], [ "Q07959-1", "IZH3", "Glycosylation_Annotation", "123", "123", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q07959" ], [ "Q07959-1", "IZH3", "Glycosylation_Annotation", "256", "256", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q07959" ], [ "Q07959-1", "IZH3", "Glycosylation_Annotation", "319", "319", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q07959" ], [ "Q07959-1", "IZH3", "Glycosylation_Annotation", "153", "153", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q07959" ], [ "P0CX69-1", "TY1A-MR2", "Site_Annotation", "401", "402", "Cleavage; by Ty1 protease", "", "HN", "", "protein_xref_uniprotkb", "P0CX69" ], [ "P0CX69-1", "TY1A-MR2", "Modified_Residue_Annotation", "416", "416", "Phosphoserine", "ECO_0000250", "S", "", "protein_xref_uniprotkb", "P0CX69" ], [ "P0CX69-1", "TY1A-MR2", "Modified_Residue_Annotation", "416", "416", "Phosphoserine", "ECO_0000250", "S", "", "protein_xref_pubmed", "Q12441" ], [ "P25379-1", "CHA1", "Modified_Residue_Annotation", "2", "2", "N-acetylserine", "ECO_0007744", "S", "", "protein_xref_uniprotkb", "P25379" ], [ "P25379-1", "CHA1", "Modified_Residue_Annotation", "2", "2", "N-acetylserine", "ECO_0007744", "S", "", "protein_xref_pubmed", "22814378" ], [ "P25379-1", "CHA1", "Modified_Residue_Annotation", "37", "37", "N6-(pyridoxal phosphate)lysine", "", "K", "", "protein_xref_uniprotkb", "P25379" ], [ "P25378-1", "RHB1", "Modified_Residue_Annotation", "206", "206", "Cysteine methyl ester", "", "C", "", "protein_xref_uniprotkb", "P25378" ], [ "P25378-1", "RHB1", "Modified_Residue_Annotation", "1", "1", "N-acetylmethionine", "ECO_0007744", "M", "", "protein_xref_uniprotkb", "P25378" ], [ "P25378-1", "RHB1", "Modified_Residue_Annotation", "1", "1", "N-acetylmethionine", "ECO_0007744", "M", "", "protein_xref_pubmed", "22814378" ], [ "P17121-1", "SAC7", "Modified_Residue_Annotation", "37", "37", "Phosphoserine", "ECO_0007744", "S", "", "protein_xref_uniprotkb", "P17121" ], [ "P17121-1", "SAC7", "Modified_Residue_Annotation", "37", "37", "Phosphoserine", "ECO_0007744", "S", "", "protein_xref_pubmed", "19779198" ], [ "P17121-1", "SAC7", "Modified_Residue_Annotation", "491", "491", "Phosphoserine", "ECO_0007744", "S", "", "protein_xref_uniprotkb", "P17121" ], [ "P17121-1", "SAC7", "Modified_Residue_Annotation", "491", "491", "Phosphoserine", "ECO_0007744", "S", "", "protein_xref_pubmed", "18407956" ], [ "P17121-1", "SAC7", "Modified_Residue_Annotation", "491", "491", "Phosphoserine", "ECO_0007744", "S", "", "protein_xref_pubmed", "19779198" ], [ "P17121-1", "SAC7", "Modified_Residue_Annotation", "491", "491", "Phosphoserine", "ECO_0007744", "S", "", "protein_xref_pubmed", "17330950" ], [ "P17121-1", "SAC7", "Modified_Residue_Annotation", "435", "435", "Phosphoserine", "ECO_0007744", "S", "", "protein_xref_uniprotkb", "P17121" ], [ "P17121-1", "SAC7", "Modified_Residue_Annotation", "435", "435", "Phosphoserine", "ECO_0007744", "S", "", "protein_xref_pubmed", "18407956" ], [ "P17121-1", "SAC7", "Modified_Residue_Annotation", "435", "435", "Phosphoserine", "ECO_0007744", "S", "", "protein_xref_pubmed", "19779198" ], [ "P17121-1", "SAC7", "Modified_Residue_Annotation", "632", "632", "Phosphoserine", "ECO_0007744", "S", "", "protein_xref_uniprotkb", "P17121" ], [ "P17121-1", "SAC7", "Modified_Residue_Annotation", "632", "632", "Phosphoserine", "ECO_0007744", "S", "", "protein_xref_pubmed", "18407956" ], [ "P17121-1", "SAC7", "Modified_Residue_Annotation", "632", "632", "Phosphoserine", "ECO_0007744", "S", "", "protein_xref_pubmed", "19779198" ], [ "P17121-1", "SAC7", "Modified_Residue_Annotation", "46", "46", "Phosphoserine", "ECO_0007744", "S", "", "protein_xref_uniprotkb", "P17121" ], [ "P17121-1", "SAC7", "Modified_Residue_Annotation", "46", "46", "Phosphoserine", "ECO_0007744", "S", "", "protein_xref_pubmed", "17330950" ], [ "P25374-1", "NFS1", "Active_Site_Annotation", "421", "421", "Cysteine persulfide intermediate", "ECO_0000250", "C", "", "protein_xref_uniprotkb", "P25374" ], [ "P25374-1", "NFS1", "Active_Site_Annotation", "421", "421", "Cysteine persulfide intermediate", "ECO_0000250", "C", "", "protein_xref_pubmed", "P0A6B7" ], [ "P25374-1", "NFS1", "Binding_Site_Annotation", "421", "421", "via persulfide group", "ECO_0000250", "C", "", "protein_xref_uniprotkb", "P25374" ], [ "P25374-1", "NFS1", "Binding_Site_Annotation", "421", "421", "via persulfide group", "ECO_0000250", "C", "", "protein_xref_pubmed", "O29689" ], [ "P25374-1", "NFS1", "Modified_Residue_Annotation", "299", "299", "N6-(pyridoxal phosphate)lysine", "ECO_0000250", "K", "", "protein_xref_uniprotkb", "P25374" ], [ "P25374-1", "NFS1", "Modified_Residue_Annotation", "299", "299", "N6-(pyridoxal phosphate)lysine", "ECO_0000250", "K", "", "protein_xref_pubmed", "P0A6B9" ], [ "P25374-1", "NFS1", "Mutagenesis_Annotation", "191", "191", "Disrupts iron-sulfur (Fe-S) cluster assembly and decreases cytosolic tRNA thiolation. Exhibits constitutive up-regulation of the genes of the cellular iron uptake system.", "ECO_0000269", "I", "S", "protein_xref_uniprotkb", "P25374" ], [ "P25374-1", "NFS1", "Mutagenesis_Annotation", "191", "191", "Disrupts iron-sulfur (Fe-S) cluster assembly and decreases cytosolic tRNA thiolation. Exhibits constitutive up-regulation of the genes of the cellular iron uptake system.", "ECO_0000269", "I", "S", "protein_xref_pubmed", "10551871" ], [ "P25374-1", "NFS1", "Mutagenesis_Annotation", "191", "191", "Disrupts iron-sulfur (Fe-S) cluster assembly and decreases cytosolic tRNA thiolation. Exhibits constitutive up-regulation of the genes of the cellular iron uptake system.", "ECO_0000269", "I", "S", "protein_xref_pubmed", "31040179" ], [ "P17123-1", "SPO12", "Modified_Residue_Annotation", "2", "2", "N-acetylserine", "ECO_0007744", "S", "", "protein_xref_uniprotkb", "P17123" ], [ "P17123-1", "SPO12", "Modified_Residue_Annotation", "2", "2", "N-acetylserine", "ECO_0007744", "S", "", "protein_xref_pubmed", "22814378" ], [ "P17123-1", "SPO12", "Modified_Residue_Annotation", "118", "118", "Phosphoserine", "ECO_0007744", "S", "", "protein_xref_uniprotkb", "P17123" ], [ "P17123-1", "SPO12", "Modified_Residue_Annotation", "118", "118", "Phosphoserine", "ECO_0007744", "S", "", "protein_xref_pubmed", "19779198" ], [ "P17123-1", "SPO12", "Modified_Residue_Annotation", "125", "125", "Phosphoserine", "ECO_0007744", "S", "", "protein_xref_uniprotkb", "P17123" ], [ "P17123-1", "SPO12", "Modified_Residue_Annotation", "125", "125", "Phosphoserine", "ECO_0007744", "S", "", "protein_xref_pubmed", "19779198" ], [ "P25371-1", "ADP1", "Glycosylation_Annotation", "221", "221", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "P25371" ], [ "P25371-1", "ADP1", "Glycosylation_Annotation", "935", "935", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "P25371" ], [ "P25371-1", "ADP1", "Glycosylation_Annotation", "50", "50", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "P25371" ], [ "P25371-1", "ADP1", "Glycosylation_Annotation", "165", "165", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "P25371" ], [ "P25371-1", "ADP1", "Glycosylation_Annotation", "114", "114", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "P25371" ], [ "P25371-1", "ADP1", "Modified_Residue_Annotation", "659", "659", "Phosphoserine", "ECO_0007744", "S", "", "protein_xref_uniprotkb", "P25371" ], [ "P25371-1", "ADP1", "Modified_Residue_Annotation", "659", "659", "Phosphoserine", "ECO_0007744", "S", "", "protein_xref_pubmed", "18407956" ], [ "P25371-1", "ADP1", "Modified_Residue_Annotation", "659", "659", "Phosphoserine", "ECO_0007744", "S", "", "protein_xref_pubmed", "19779198" ], [ "P25371-1", "ADP1", "Modified_Residue_Annotation", "702", "702", "Phosphoserine", "ECO_0007744", "S", "", "protein_xref_uniprotkb", "P25371" ], [ "P25371-1", "ADP1", "Modified_Residue_Annotation", "702", "702", "Phosphoserine", "ECO_0007744", "S", "", "protein_xref_pubmed", "18407956" ], [ "P25371-1", "ADP1", "Modified_Residue_Annotation", "702", "702", "Phosphoserine", "ECO_0007744", "S", "", "protein_xref_pubmed", "19779198" ], [ "P25373-1", "GRX1", "Disulfide_Bond_Annotation", "27", "27", "Redox-active; alternate", "ECO_0000269", "C", "", "protein_xref_uniprotkb", "P25373" ], [ "P25373-1", "GRX1", "Disulfide_Bond_Annotation", "27", "27", "Redox-active; alternate", "ECO_0000269", "C", "", "protein_xref_pubmed", "18473363" ], [ "P25373-1", "GRX1", "Disulfide_Bond_Annotation", "30", "30", "Redox-active; alternate", "ECO_0000269", "C", "", "protein_xref_uniprotkb", "P25373" ], [ "P25373-1", "GRX1", "Disulfide_Bond_Annotation", "30", "30", "Redox-active; alternate", "ECO_0000269", "C", "", "protein_xref_pubmed", "18473363" ], [ "P25373-1", "GRX1", "Modified_Residue_Annotation", "27", "27", "S-glutathionyl cysteine; alternate", "ECO_0000269", "C", "", "protein_xref_uniprotkb", "P25373" ], [ "P25373-1", "GRX1", "Modified_Residue_Annotation", "27", "27", "S-glutathionyl cysteine; alternate", "ECO_0000269", "C", "", "protein_xref_pubmed", "18473363" ], [ "P25373-1", "GRX1", "Modified_Residue_Annotation", "27", "27", "S-glutathionyl cysteine; alternate", "ECO_0000269", "C", "", "protein_xref_pubmed", "17327665" ], [ "P25373-1", "GRX1", "Mutagenesis_Annotation", "30", "30", "Leads to increased oxidoreductase activity.", "ECO_0000269", "C", "S", "protein_xref_uniprotkb", "P25373" ], [ "P25373-1", "GRX1", "Mutagenesis_Annotation", "30", "30", "Leads to increased oxidoreductase activity.", "ECO_0000269", "C", "S", "protein_xref_pubmed", "18992757" ], [ "P25373-1", "GRX1", "Mutagenesis_Annotation", "89", "89", "Leads to increased oxidoreductase activity.", "ECO_0000269", "D", "S", "protein_xref_uniprotkb", "P25373" ], [ "P25373-1", "GRX1", "Mutagenesis_Annotation", "89", "89", "Leads to increased oxidoreductase activity.", "ECO_0000269", "D", "S", "protein_xref_pubmed", "20417731" ], [ "P25372-1", "TRX3", "Active_Site_Annotation", "58", "58", "Nucleophile", "", "C", "", "protein_xref_uniprotkb", "P25372" ], [ "P25372-1", "TRX3", "Active_Site_Annotation", "55", "55", "Nucleophile", "", "C", "", "protein_xref_uniprotkb", "P25372" ], [ "P25372-1", "TRX3", "Site_Annotation", "56", "56", "Contributes to redox potential value", "", "G", "", "protein_xref_uniprotkb", "P25372" ], [ "P25372-1", "TRX3", "Site_Annotation", "49", "49", "Deprotonates C-terminal active site Cys", "", "D", "", "protein_xref_uniprotkb", "P25372" ], [ "P25372-1", "TRX3", "Site_Annotation", "57", "57", "Contributes to redox potential value", "", "P", "", "protein_xref_uniprotkb", "P25372" ], [ "P25372-1", "TRX3", "Disulfide_Bond_Annotation", "58", "58", "Redox-active", "ECO_0000255", "C", "", "protein_xref_uniprotkb", "P25372" ], [ "P25372-1", "TRX3", "Disulfide_Bond_Annotation", "58", "58", "Redox-active", "ECO_0000255", "C", "", "protein_xref_pubmed", "PRU00691" ], [ "P25372-1", "TRX3", "Disulfide_Bond_Annotation", "55", "55", "Redox-active", "ECO_0000255", "C", "", "protein_xref_uniprotkb", "P25372" ], [ "P25372-1", "TRX3", "Disulfide_Bond_Annotation", "55", "55", "Redox-active", "ECO_0000255", "C", "", "protein_xref_pubmed", "PRU00691" ], [ "Q06563-1", "SYM1", "Mutagenesis_Annotation", "172", "172", "Loss of function.", "ECO_0000269", "N", "K", "protein_xref_uniprotkb", "Q06563" ], [ "Q06563-1", "SYM1", "Mutagenesis_Annotation", "172", "172", "Loss of function.", "ECO_0000269", "N", "K", "protein_xref_pubmed", "16582910" ], [ "Q06563-1", "SYM1", "Mutagenesis_Annotation", "54", "54", "Almost abolishes function.", "ECO_0000269", "R", "Q", "protein_xref_uniprotkb", "Q06563" ], [ "Q06563-1", "SYM1", "Mutagenesis_Annotation", "54", "54", "Almost abolishes function.", "ECO_0000269", "R", "Q", "protein_xref_pubmed", "16582910" ], [ "Q06563-1", "SYM1", "Mutagenesis_Annotation", "54", "54", "Loss of function.", "ECO_0000269", "R", "W", "protein_xref_uniprotkb", "Q06563" ], [ "Q06563-1", "SYM1", "Mutagenesis_Annotation", "54", "54", "Loss of function.", "ECO_0000269", "R", "W", "protein_xref_pubmed", "16582910" ] ] }, "readme": "Name\n - Yeast Protein Site Annotation\n\nVersion\n - v-2.2.1\n\nCreated on\n - 2022-08-31T11:08:19.037259\n\nModified on\n - 2023-09-11T19:24:27\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu]\n\nAuthors\n - Maria Martin [martin@ebi.ac.uk], Preethi Vasudev [pvasudev@ebi.ac.uk]\n\nChecksum\n - \n\nUsability Domain\n - The Yeast Protein Site Annotation (UniProtKB) dataset contains yeast [taxid:559292] site annotations for UniProtKB canonical accessions. The dataset contains information about UniProtKB annotations with their amino acid range. If you use this dataset please give proper attribution to UniProtKB and GlyGen\n\nDescription Domain\n Keywords\n - site annotation\n - amino acid range\n - UniProtKB\n\n Pipeline Steps\n - Step-1: The script extracts the site annotation triples from the triplestore for the UniProtKB canonical sequnces asnd extracts as a dataset in a csv format\n\nExecution Domain\n Scripts - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/make-protein-dataset.py\n\n\n Software Prerequisites\n Name: Python\n Version: 2.7.5\n URI: https://www.python.org/download/releases/2.7.5/\n\nI/O Domain\n Input Subdomain\n Name: yeast_protein_masterlist.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/yeast_protein_masterlist.csv\n Name: uniprot-proteome-saccharomyces-cerevisiae.nt\n URI: https:/data.glygen.org/ln2downloads/ebi/2023_10_30/uniprot-proteome-saccharomyces-cerevisiae.nt\n Output Subdomain\n Name: yeast_protein_site_annotation_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/yeast_protein_site_annotation_uniprotkb.csv\n Name: yeast_protein_site_annotation_uniprotkb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/yeast_protein_site_annotation_uniprotkb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"3606\"\n Name: \"gene_symbol\"\n Description: \"\"Official gene name/symbol assigned to the gene. Human gene names/symbols are approved by the HUGO Gene Nomenclature Committee (HGNC)\"\n Unique Values: \"3417\"\n Name: \"ann_type\"\n Description: \"Annotation Type\"\n Unique Values: \"10\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"1467\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"1473\"\n Name: \"annotation\"\n Description: \"Function annotation from UniProtKB|RefSeq database\"\n Unique Values: \"4146\"\n Name: \"ecoid\"\n Description: \"Evidence & Conclusion Ontology (ECO) identifier\"\n Unique Values: \"7\"\n Name: \"ref_aa\"\n Description: \"Reference amino acid residue\"\n Unique Values: \"589\"\n Name: \"alt_aa\"\n Description: \"Altered amino acid residue\"\n Unique Values: \"230\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"2\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"5913\"", "downloadurl": "/ln2data/releases/data/v-2.2.1/reviewed/yeast_protein_site_annotation_uniprotkb.csv" }