{ "bcoid": "GLY_000859", "title": "Dicty Protein Site Annotation", "description": "The Dicty Protein Site Annotation (UniProtKB) dataset contains dicty [taxid:44689] site annotations for ...", "filename": "dicty_protein_site_annotation_uniprotkb.csv", "filetype": "csv", "categories": { "species": [ "Dictyostelium discoideum" ], "molecule": [ "Protein" ], "tag": [ "Site annotation" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "Q54PT3-1...", "cyp556A1..." ], [ "Q54PT9-1...", "mrfA..." ] ], "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" } ], [ "Q54PT3-1", "cyp556A1", "Binding_Site_Annotation", "587", "587", "axial binding residue", "", "C", "", "protein_xref_uniprotkb", "Q54PT3" ], [ "Q54PT9-1", "mrfA", "Nucleotide_Binding_Annotation", "286", "546", "NDT80", "ECO_0000255", "PNLSPTNSPIQSPHLPTDNYLMIGSENENSDPPSPMTQYNENPPFTWTDYKSEPWYTTFNTNGDEMPVPLLNIMASKGFSYIGGQWIYCRRNHFQLDITAVYPKLFQETQYGHNGVTLSNSSSSVDPTQTPSYMLISGVKTPINGLTLTIKGIKNRADMSQQESEVELFQTNSKREKQGEHAPKPVAIQFGSLVSIQRLHFRKATLNNARRHGQPNPHQEFNQLVVSLYGRCMGQEYCIVSYVSPALIVRTATQVTPPGDL", "", "protein_xref_uniprotkb", "Q54PT9" ], [ "Q54PT9-1", "mrfA", "Mutagenesis_Annotation", "376", "376", "Loss of binding to ecmA promoter.", "ECO_0000269", "R", "A", "protein_xref_uniprotkb", "Q54PT9" ], [ "Q54PT9-1", "mrfA", "Mutagenesis_Annotation", "376", "376", "Loss of binding to ecmA promoter.", "ECO_0000269", "R", "A", "protein_xref_pubmed", "22811266" ], [ "Q54PT9-1", "mrfA", "Mutagenesis_Annotation", "460", "460", "Loss of binding to ecmA promoter.", "ECO_0000269", "R", "A", "protein_xref_uniprotkb", "Q54PT9" ], [ "Q54PT9-1", "mrfA", "Mutagenesis_Annotation", "460", "460", "Loss of binding to ecmA promoter.", "ECO_0000269", "R", "A", "protein_xref_pubmed", "22811266" ], [ "Q54N47-1", "bcaA", "Modified_Residue_Annotation", "213", "213", "N6-(pyridoxal phosphate)lysine", "", "K", "", "protein_xref_uniprotkb", "Q54N47" ], [ "Q86AV4-1", "expl5", "Glycosylation_Annotation", "89", "89", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q86AV4" ], [ "Q55BJ6-1", "plbB", "Glycosylation_Annotation", "138", "138", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q55BJ6" ], [ "Q55BJ6-1", "plbB", "Glycosylation_Annotation", "427", "427", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q55BJ6" ], [ "Q55BJ6-1", "plbB", "Glycosylation_Annotation", "544", "544", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q55BJ6" ], [ "Q55BJ6-1", "plbB", "Glycosylation_Annotation", "219", "219", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q55BJ6" ], [ "Q55BJ6-1", "plbB", "Glycosylation_Annotation", "73", "73", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q55BJ6" ], [ "Q55BJ6-1", "plbB", "Glycosylation_Annotation", "564", "564", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q55BJ6" ], [ "Q54JJ8-1", "", "Active_Site_Annotation", "70", "70", "Nucleophile", "ECO_0000256", "S", "", "protein_xref_uniprotkb", "Q54JJ8" ], [ "Q54JJ8-1", "", "Active_Site_Annotation", "195", "195", "Proton acceptor", "ECO_0000256", "D", "", "protein_xref_uniprotkb", "Q54JJ8" ], [ "Q9U3X4-1", "sdhA", "Active_Site_Annotation", "318", "318", "Proton acceptor", "ECO_0000250", "R", "", "protein_xref_uniprotkb", "Q9U3X4" ], [ "Q9U3X4-1", "sdhA", "Modified_Residue_Annotation", "77", "77", "Tele-8alpha-FAD histidine", "ECO_0000250", "H", "", "protein_xref_uniprotkb", "Q9U3X4" ], [ "P22887-1", "ndkC-1", "Active_Site_Annotation", "122", "122", "Pros-phosphohistidine intermediate", "", "H", "", "protein_xref_uniprotkb", "P22887" ], [ "Q86CZ2-1", "dhkK", "Modified_Residue_Annotation", "825", "825", "Phosphohistidine; by autocatalysis", "ECO_0000255", "H", "", "protein_xref_uniprotkb", "Q86CZ2" ], [ "Q86CZ2-1", "dhkK", "Modified_Residue_Annotation", "1125", "1125", "4-aspartylphosphate", "ECO_0000255", "D", "", "protein_xref_uniprotkb", "Q86CZ2" ], [ "Q869X2-1", "pks17", "Active_Site_Annotation", "968", "968", "Proton acceptor; for dehydratase activity", "ECO_0000255", "H", "", "protein_xref_uniprotkb", "Q869X2" ], [ "Q869X2-1", "pks17", "Active_Site_Annotation", "641", "641", "For acyl/malonyl transferase activity", "ECO_0000255", "S", "", "protein_xref_uniprotkb", "Q869X2" ], [ "Q869X2-1", "pks17", "Active_Site_Annotation", "1132", "1132", "Proton donor; for dehydratase activity", "ECO_0000255", "D", "", "protein_xref_uniprotkb", "Q869X2" ], [ "Q869X2-1", "pks17", "Active_Site_Annotation", "179", "179", "For beta-ketoacyl synthase activity", "ECO_0000255", "C", "", "protein_xref_uniprotkb", "Q869X2" ], [ "Q869X2-1", "pks17", "Active_Site_Annotation", "316", "316", "For beta-ketoacyl synthase activity", "ECO_0000255", "H", "", "protein_xref_uniprotkb", "Q869X2" ], [ "Q869X2-1", "pks17", "Active_Site_Annotation", "356", "356", "For beta-ketoacyl synthase activity", "ECO_0000255", "H", "", "protein_xref_uniprotkb", "Q869X2" ], [ "Q869X2-1", "pks17", "Modified_Residue_Annotation", "2544", "2544", "O-(pantetheine 4'-phosphoryl)serine", "ECO_0000255", "S", "", "protein_xref_uniprotkb", "Q869X2" ], [ "Q869X3-1", "", "Active_Site_Annotation", "147", "147", "Proton acceptor", "ECO_0000255", "D", "", "protein_xref_uniprotkb", "Q869X3" ], [ "Q869X7-1", "", "Active_Site_Annotation", "279", "279", "Proton donor/acceptor", "ECO_0000250", "E", "", "protein_xref_uniprotkb", "Q869X7" ], [ "Q869X7-1", "", "Site_Annotation", "198", "198", "Interaction with histone H4 N-terminus", "ECO_0000250", "W", "", "protein_xref_uniprotkb", "Q869X7" ], [ "Q869X5-1", "", "Active_Site_Annotation", "535", "535", "Proton donor/acceptor", "ECO_0000256", "E", "", "protein_xref_uniprotkb", "Q869X5" ], [ "Q55DK2-1", "", "Active_Site_Annotation", "349", "349", "Proton acceptor", "ECO_0000255", "D", "", "protein_xref_uniprotkb", "Q55DK2" ], [ "Q55GK3-1", "mybM", "Nucleotide_Binding_Annotation", "90", "114", "H-T-H motif", "ECO_0000255", "WKRISAEMGGQKTGAQCAQHWKRVL", "", "protein_xref_uniprotkb", "Q55GK3" ], [ "Q55GK3-1", "mybM", "Nucleotide_Binding_Annotation", "142", "166", "H-T-H motif", "ECO_0000255", "WKKIAKRICKRTDIQCRYQYLKSLQ", "", "protein_xref_uniprotkb", "Q55GK3" ], [ "Q55GK8-1", "kil1", "Glycosylation_Annotation", "344", "344", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q55GK8" ], [ "Q55GK8-1", "kil1", "Glycosylation_Annotation", "47", "47", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q55GK8" ], [ "Q55GK8-1", "kil1", "Glycosylation_Annotation", "324", "324", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q55GK8" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "2858", "2858", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "2128", "2128", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "2781", "2781", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "991", "991", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "110", "110", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "1229", "1229", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "2243", "2243", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "3390", "3390", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "2838", "2838", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "2145", "2145", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "2787", "2787", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "2378", "2378", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "1381", "1381", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "1247", "1247", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "2572", "2572", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "2714", "2714", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "1054", "1054", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "3666", "3666", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "845", "845", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "258", "258", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "3459", "3459", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "2800", "2800", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "3372", "3372", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "2453", "2453", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "2351", "2351", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "3130", "3130", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "3083", "3083", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "2516", "2516", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "2493", "2493", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "1769", "1769", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "2496", "2496", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "3466", "3466", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "2624", "2624", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "1815", "1815", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "284", "284", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "652", "652", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "2601", "2601", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "43", "43", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "2668", "2668", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "2294", "2294", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "3681", "3681", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "672", "672", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "2698", "2698", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "3557", "3557", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q8T2A1-1", "colB", "Glycosylation_Annotation", "3676", "3676", "N-linked (GlcNAc...) asparagine", "", "N", "", "protein_xref_uniprotkb", "Q8T2A1" ], [ "Q54EX5-1", "sptB", "Modified_Residue_Annotation", "321", "321", "N6-(pyridoxal phosphate)lysine", "", "K", "", "protein_xref_uniprotkb", "Q54EX5" ] ] }, "readme": "Name\n - Dicty Protein Site Annotation\n\nVersion\n - v-2.4.1\n\nCreated on\n - \n\nModified on\n - 2024-01-09T05:12:01\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Luke Johnson [luke.johnson@email.gwu.edu], Urnisha Bhuiyan [sbhuiyan28@email.gwu.edu], Cyrus Au-Yeung [cyruschauyeung@gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu]\n\nAuthors\n - \n\nChecksum\n - \n\nUsability Domain\n - The Dicty Protein Site Annotation (UniProtKB) dataset contains dicty [taxid:44689] site annotations for UniProtKB canonical accessions. The dataset contains information about UniProtKB annotations with their amino acid range. The dataset is derived form 2019-09 UniprotKB release. 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: dicty_protein_masterlist.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/dicty_protein_masterlist.csv\n Name: uniprot-proteome-dictyostelium-discoideum.nt\n URI: https:/data.glygen.org/ln2downloads/ebi/2024_02_19/uniprot-proteome-dictyostelium-discoideum.nt\n Output Subdomain\n Name: dicty_protein_site_annotation_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/dicty_protein_site_annotation_uniprotkb.csv\n Name: dicty_protein_site_annotation_uniprotkb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/dicty_protein_site_annotation_uniprotkb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"1389\"\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: \"1035\"\n Name: \"ann_type\"\n Description: \"Annotation Type\"\n Unique Values: \"9\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"1348\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"1345\"\n Name: \"annotation\"\n Description: \"Function annotation from UniProtKB|RefSeq database\"\n Unique Values: \"381\"\n Name: \"ecoid\"\n Description: \"Evidence & Conclusion Ontology (ECO) identifier\"\n Unique Values: \"9\"\n Name: \"ref_aa\"\n Description: \"Reference amino acid residue\"\n Unique Values: \"148\"\n Name: \"alt_aa\"\n Description: \"Altered amino acid residue\"\n Unique Values: \"38\"\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: \"1480\"", "downloadurl": "/ln2data/releases/data/v-2.4.1/reviewed/dicty_protein_site_annotation_uniprotkb.csv" }