{ "bcoid": "GLY_000853", "title": "Dicty Protein PTM Annotation (UniProtKB)", "description": "The Dicty Protein PTM Annotation (UniProtKB) dataset contains dicty [taxid:44689] PTM annotations for ...", "filename": "dicty_protein_ptm_annotation_uniprotkb.csv", "filetype": "csv", "categories": { "species": [ "Dictyostelium discoideum" ], "molecule": [ "Protein" ], "tag": [ "PTM annotation" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "Q94504-1...", "protein_xref..." ], [ "Q94504-1...", "protein_xref..." ] ], "headers": [ "uniprotkb_ca...", "xref_key..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "eco_id" }, { "type": "string", "label": "ptm_annotation" } ], [ "Q94504-1", "protein_xref_uniprotkb", "Q94504", "ECO_0000269", "Glycosylated; contains GlcNAc-alpha-1-P-Ser residues. Also N-glycosylated." ], [ "Q94504-1", "protein_xref_pubmed", "9056234", "ECO_0000269", "Glycosylated; contains GlcNAc-alpha-1-P-Ser residues. Also N-glycosylated." ], [ "P42526-1", "protein_xref_uniprotkb", "P42526", "ECO_0000269", "Phosphorylated." ], [ "P42526-1", "protein_xref_pubmed", "7822284", "ECO_0000269", "Phosphorylated." ], [ "O00910-1", "protein_xref_uniprotkb", "O00910", "ECO_0000269", "Tyrosine phosphorylated in response to cAMP. Not tyrosine phosphorylated in growing cells. Tyrosine phosphorylation is first detected at the tight mound stage, continues throughout the slug stage and early culmination, and starts to decrease at mid-culmination. Barely detectable in fruiting bodies." ], [ "O00910-1", "protein_xref_pubmed", "9670017", "ECO_0000269", "Tyrosine phosphorylated in response to cAMP. Not tyrosine phosphorylated in growing cells. Tyrosine phosphorylation is first detected at the tight mound stage, continues throughout the slug stage and early culmination, and starts to decrease at mid-culmination. Barely detectable in fruiting bodies." ], [ "P13231-1", "protein_xref_uniprotkb", "P13231", "ECO_0000269", "Phosphorylated." ], [ "P13231-1", "protein_xref_pubmed", "7822284", "ECO_0000269", "Phosphorylated." ], [ "Q9XYS8-1", "protein_xref_uniprotkb", "Q9XYS8", "ECO_0000269", "Heavily glycosylated." ], [ "Q9XYS8-1", "protein_xref_pubmed", "11489884", "ECO_0000269", "Heavily glycosylated." ], [ "P16051-1", "protein_xref_uniprotkb", "P16051", "ECO_0000269", "Ser-113 is transiently phosphorylated following stimulation with extracellular cAMP." ], [ "P16051-1", "protein_xref_pubmed", "8063709", "ECO_0000269", "Ser-113 is transiently phosphorylated following stimulation with extracellular cAMP." ], [ "Q54R82-1", "protein_xref_uniprotkb", "Q54R82", "ECO_0000269", "ubcB and ubpB differentially control ubiquitination/deubiquitination and degradation in a cell-type-specific and temporally regulated manner." ], [ "Q54R82-1", "protein_xref_pubmed", "9832508", "ECO_0000269", "ubcB and ubpB differentially control ubiquitination/deubiquitination and degradation in a cell-type-specific and temporally regulated manner." ], [ "Q968Z6-1", "protein_xref_uniprotkb", "Q968Z6", "ECO_0000269", "N-glycosylated." ], [ "Q968Z6-1", "protein_xref_pubmed", "10493938", "ECO_0000269", "N-glycosylated." ], [ "Q54QM6-1", "protein_xref_uniprotkb", "Q54QM6", "ECO_0000305", "Phosphorylated." ], [ "Q54QM6-1", "protein_xref_pubmed", "15351882", "ECO_0000305", "Phosphorylated." ], [ "Q23892-1", "protein_xref_uniprotkb", "Q23892", "ECO_0000269", "Glycosylated. The polyoligosaccharides are of the high-mannose type and are highly substituted with both phosphate and sulfate moieties." ], [ "Q23892-1", "protein_xref_pubmed", "6228551", "ECO_0000269", "Glycosylated. The polyoligosaccharides are of the high-mannose type and are highly substituted with both phosphate and sulfate moieties." ], [ "P13773-1", "protein_xref_uniprotkb", "P13773", "ECO_0000269", "C-terminal Ser or Thr residues may be phosphorylated." ], [ "P13773-1", "protein_xref_pubmed", "7721769", "ECO_0000269", "C-terminal Ser or Thr residues may be phosphorylated." ], [ "P13773-1", "protein_xref_pubmed", "9880518", "ECO_0000269", "C-terminal Ser or Thr residues may be phosphorylated." ], [ "P13773-1", "protein_xref_pubmed", "8120068", "ECO_0000269", "C-terminal Ser or Thr residues may be phosphorylated." ], [ "Q23917-1", "protein_xref_uniprotkb", "Q23917", "ECO_0000269", "The phosphorelay mechanism involves the sequential transfer of a phosphate group from Asp-212 of pde2 to 'His-65' of rdeA. Phosphorylation of Asp-212 activates the phosphodiesterase domain." ], [ "Q23917-1", "protein_xref_pubmed", "10488068", "ECO_0000269", "The phosphorelay mechanism involves the sequential transfer of a phosphate group from Asp-212 of pde2 to 'His-65' of rdeA. Phosphorylation of Asp-212 activates the phosphodiesterase domain." ], [ "Q8T1G4-1", "protein_xref_uniprotkb", "Q8T1G4", "ECO_0000269", "Contains six disulfide bonds." ], [ "Q8T1G4-1", "protein_xref_pubmed", "15640146", "ECO_0000269", "Contains six disulfide bonds." ], [ "Q54BX3-1", "protein_xref_uniprotkb", "Q54BX3", "ECO_0000269", "Ubiquitinated (Probable). Degraded by the proteasome; degradation is stimulated by polyglutamine (polyQ) aggregates (PubMed:30029002)." ], [ "Q54BX3-1", "protein_xref_pubmed", "30029002", "ECO_0000269", "Ubiquitinated (Probable). Degraded by the proteasome; degradation is stimulated by polyglutamine (polyQ) aggregates (PubMed:30029002)." ], [ "Q95ZG8-1", "protein_xref_uniprotkb", "Q95ZG8", "ECO_0000269", "This protein is thought to be subject to lipidation, and this requires phlp1." ], [ "Q95ZG8-1", "protein_xref_pubmed", "16135826", "ECO_0000269", "This protein is thought to be subject to lipidation, and this requires phlp1." ], [ "P13723-1", "protein_xref_uniprotkb", "P13723", "ECO_0000269", "N-glycosylated." ], [ "P13723-1", "protein_xref_pubmed", "2972716", "ECO_0000269", "N-glycosylated." ], [ "Q55D99-1", "protein_xref_uniprotkb", "Q55D99", "ECO_0000269", "Phosphorylation on Thr-585 results in cAMP-mediated activation and localization to the cytoskeleton." ], [ "Q55D99-1", "protein_xref_pubmed", "11389841", "ECO_0000269", "Phosphorylation on Thr-585 results in cAMP-mediated activation and localization to the cytoskeleton." ], [ "Q55CL6-1", "protein_xref_uniprotkb", "Q55CL6", "ECO_0000269", "Sumoylated and ubiquitinated in response to chemoattractant stimulation. Sumoylation is linked to kinase activation and results in translocation." ], [ "Q55CL6-1", "protein_xref_pubmed", "12062087", "ECO_0000269", "Sumoylated and ubiquitinated in response to chemoattractant stimulation. Sumoylation is linked to kinase activation and results in translocation." ], [ "P12729-1", "protein_xref_uniprotkb", "P12729", "ECO_0000269", "O-glycosylated in the repeat region. The oligosaccharides contain N-acetylglucosamine and fucose as the major constituents." ], [ "P12729-1", "protein_xref_pubmed", "8404891", "ECO_0000269", "O-glycosylated in the repeat region. The oligosaccharides contain N-acetylglucosamine and fucose as the major constituents." ], [ "P12729-1", "protein_xref_pubmed", "8681966", "ECO_0000269", "O-glycosylated in the repeat region. The oligosaccharides contain N-acetylglucosamine and fucose as the major constituents." ], [ "Q55DL0-1", "protein_xref_uniprotkb", "Q55DL0", "ECO_0000269", "Carboxylation allows a single lysine to coordinate two zinc ions." ], [ "Q55DL0-1", "protein_xref_pubmed", "16517602", "ECO_0000269", "Carboxylation allows a single lysine to coordinate two zinc ions." ], [ "Q54XY4-1", "protein_xref_uniprotkb", "Q54XY4", "ECO_0000269", "Phosphorylated at Ser-359 by PKB and PKBR1 is induced by chemoattractant (PubMed:20493808)." ], [ "Q54XY4-1", "protein_xref_pubmed", "20493808", "ECO_0000269", "Phosphorylated at Ser-359 by PKB and PKBR1 is induced by chemoattractant (PubMed:20493808)." ], [ "P52285-1", "protein_xref_uniprotkb", "P52285", "ECO_0000269", "Hydroxylated by phyA." ], [ "P52285-1", "protein_xref_pubmed", "12244067", "ECO_0000269", "Hydroxylated by phyA." ], [ "P52285-1", "protein_xref_pubmed", "9660787", "ECO_0000269", "Hydroxylated by phyA." ], [ "Q54XQ2-1", "protein_xref_uniprotkb", "Q54XQ2", "ECO_0000269", "Autophosphorylated." ], [ "Q54XQ2-1", "protein_xref_pubmed", "12686622", "ECO_0000269", "Autophosphorylated." ], [ "Q54WT8-1", "protein_xref_uniprotkb", "Q54WT8", "ECO_0000269", "Glycosylated and non-glycosylated forms exist throughout all developmental stages." ], [ "Q54WT8-1", "protein_xref_pubmed", "22262860", "ECO_0000269", "Glycosylated and non-glycosylated forms exist throughout all developmental stages." ], [ "Q9BKJ9-1", "protein_xref_uniprotkb", "Q9BKJ9", "ECO_0000269", "Heavily glycosylated." ], [ "Q9BKJ9-1", "protein_xref_pubmed", "11489884", "ECO_0000269", "Heavily glycosylated." ], [ "P34114-1", "protein_xref_uniprotkb", "P34114", "ECO_0000269", "Enzyme activity requires processing of the 113 kDa peptide to an enzymatically active 106 kDa form of the protein. Processing would occur near the middle of the Gln-rich repetitive element." ], [ "P34114-1", "protein_xref_pubmed", "1310312", "ECO_0000269", "Enzyme activity requires processing of the 113 kDa peptide to an enzymatically active 106 kDa form of the protein. Processing would occur near the middle of the Gln-rich repetitive element." ], [ "O77257-1", "protein_xref_uniprotkb", "O77257", "ECO_0000305", "Probably contains disulfide bonds." ], [ "O77257-1", "protein_xref_pubmed", "27187592", "ECO_0000305", "Probably contains disulfide bonds." ], [ "P25323-1", "protein_xref_uniprotkb", "P25323", "ECO_0000269", "Autophosphorylated. Transiently phosphorylated on Thr-166 and Thr-289. This phosphorylation is gbpC-dependent." ], [ "P25323-1", "protein_xref_pubmed", "16546177", "ECO_0000269", "Autophosphorylated. Transiently phosphorylated on Thr-166 and Thr-289. This phosphorylation is gbpC-dependent." ], [ "Q54VI3-1", "protein_xref_uniprotkb", "Q54VI3", "ECO_0000269", "(Microbial infection) ADP-ribosylated at Arg-763 by the Legionella pneumophila effector Lart1, which inhibits the glutamate dehydrogenase activity. Amoeba are natural hosts of Legionella, and ADP-ribosylation by Lart1 may promote Legionella parasitism." ], [ "Q54VI3-1", "protein_xref_pubmed", "33476647", "ECO_0000269", "(Microbial infection) ADP-ribosylated at Arg-763 by the Legionella pneumophila effector Lart1, which inhibits the glutamate dehydrogenase activity. Amoeba are natural hosts of Legionella, and ADP-ribosylation by Lart1 may promote Legionella parasitism." ], [ "Q9NCL8-1", "protein_xref_uniprotkb", "Q9NCL8", "ECO_0000269", "Phosphorylated in response to activation of rasG." ], [ "Q9NCL8-1", "protein_xref_pubmed", "15352238", "ECO_0000269", "Phosphorylated in response to activation of rasG." ], [ "P08799-1", "protein_xref_uniprotkb", "P08799", "ECO_0000269", "Phosphorylation inhibits thick filament formation and reduces the actin-activated ATPase activity." ], [ "P08799-1", "protein_xref_pubmed", "2387408", "ECO_0000269", "Phosphorylation inhibits thick filament formation and reduces the actin-activated ATPase activity." ], [ "P08799-1", "protein_xref_pubmed", "2828113", "ECO_0000269", "Phosphorylation inhibits thick filament formation and reduces the actin-activated ATPase activity." ], [ "Q55FQ9-1", "protein_xref_uniprotkb", "Q55FQ9", "ECO_0000269", "Heavily glycosylated." ], [ "Q55FQ9-1", "protein_xref_pubmed", "11489884", "ECO_0000269", "Heavily glycosylated." ], [ "O76856-1", "protein_xref_uniprotkb", "O76856", "ECO_0000269", "N-glycosylated on 2 out of the 3 potential sites. Glycans contain sulfated Mannose." ], [ "O76856-1", "protein_xref_pubmed", "10523518", "ECO_0000269", "N-glycosylated on 2 out of the 3 potential sites. Glycans contain sulfated Mannose." ], [ "Q869N2-1", "protein_xref_uniprotkb", "Q869N2", "ECO_0000269", "Autophosphorylated at Ser-8. This may stimulate interaction with GTP-bound Rac family members which then further stimulates autophosphorylation and kinase activity." ], [ "Q869N2-1", "protein_xref_pubmed", "9774403", "ECO_0000269", "Autophosphorylated at Ser-8. This may stimulate interaction with GTP-bound Rac family members which then further stimulates autophosphorylation and kinase activity." ], [ "Q557E4-1", "protein_xref_uniprotkb", "Q557E4", "ECO_0000269", "Hydroxylated by phyA." ], [ "Q557E4-1", "protein_xref_pubmed", "12244067", "ECO_0000269", "Hydroxylated by phyA." ], [ "Q557E4-1", "protein_xref_pubmed", "9660787", "ECO_0000269", "Hydroxylated by phyA." ], [ "Q54BD4-1", "protein_xref_uniprotkb", "Q54BD4", "ECO_0000269", "Tyrosine phosphorylated in response to the chlorinated hexaphenone DIF. Minimally phosphorylated in the absence of DIF. Phosphorylation increases during development, is highest during the slug stage, with a strong decrease at culmination." ], [ "Q54BD4-1", "protein_xref_pubmed", "11336701", "ECO_0000269", "Tyrosine phosphorylated in response to the chlorinated hexaphenone DIF. Minimally phosphorylated in the absence of DIF. Phosphorylation increases during development, is highest during the slug stage, with a strong decrease at culmination." ], [ "Q869S5-1", "protein_xref_uniprotkb", "Q869S5", "ECO_0000269", "Under osmotic stress conditions, this protein undergoes phosphorylation at a serine residue in the kinase core, which is not due to an autophosphorylation of dokA. This is in contrast to the classic two-component paradigm, which predicts only histidine and aspartate phosphorylation." ], [ "Q869S5-1", "protein_xref_pubmed", "11299049", "ECO_0000269", "Under osmotic stress conditions, this protein undergoes phosphorylation at a serine residue in the kinase core, which is not due to an autophosphorylation of dokA. This is in contrast to the classic two-component paradigm, which predicts only histidine and aspartate phosphorylation." ], [ "Q55GN6-1", "protein_xref_uniprotkb", "Q55GN6", "ECO_0000305", "Phosphorylated at Thr-262 by pkgB." ], [ "Q55GN6-1", "protein_xref_pubmed", "18635356", "ECO_0000305", "Phosphorylated at Thr-262 by pkgB." ], [ "Q8SSQ0-1", "protein_xref_uniprotkb", "Q8SSQ0", "ECO_0000269", "Phosphorylated on threonine residues." ], [ "Q8SSQ0-1", "protein_xref_pubmed", "15352238", "ECO_0000269", "Phosphorylated on threonine residues." ] ] }, "readme": "Name\n - Dicty Protein PTM Annotation (UniProtKB)\n\nVersion\n - v-2.3.1\n\nCreated on\n - \n\nModified on\n - 2024-01-09T05:01:49\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu]\n\nAuthors\n - \n\nChecksum\n - \n\nUsability Domain\n - The Dicty Protein PTM Annotation (UniProtKB) dataset contains dicty [taxid:44689] PTM annotations for UniProtKB canonical accessions. The annotation is the curated statements of mainly about glycosylation and phosphorylation. 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 - ptm annotation\n - glycosylation\n - phosphorylation\n\n Pipeline Steps\n - Step-1: The script extracts the ptm annotation strings 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: uniprot-proteome-dictyostelium-discoideum.nt\n URI: https:/data.glygen.org/ln2downloads/ebi/2023_10_30/uniprot-proteome-dictyostelium-discoideum.nt\n Output Subdomain\n Name: dicty_protein_ptm_annotation_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/dicty_protein_ptm_annotation_uniprotkb.csv\n Name: dicty_protein_ptm_annotation_uniprotkb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/dicty_protein_ptm_annotation_uniprotkb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"42\"\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: \"84\"\n Name: \"eco_id\"\n Description: \"Evidence & Conclusion Ontology (ECO) identifier\"\n Unique Values: \"2\"\n Name: \"ptm_annotation\"\n Description: \"The Post Translational Modifiaction (PTM) annotation in UniProtKB that provides more context and description about the PTMs occuring on a proein\"\n Unique Values: \"36\"", "downloadurl": "/ln2data/releases/data/v-2.3.1/reviewed/dicty_protein_ptm_annotation_uniprotkb.csv" }