{ "bcoid": "GLY_000836", "title": "Dicty Protein Enzyme Annotation (UniProtKB)", "description": "The Dicty Protein Enzyme Annotation (UniProtKB) dataset contains dicty [taxid:44689] enzyme annotations ...", "filename": "dicty_protein_enzyme_annotation_uniprotkb.csv", "filetype": "csv", "categories": { "species": [ "Dictyostelium discoideum" ], "molecule": [ "Protein" ], "tag": [ "Enzyme Annotation" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "Q54D04-1...", "1.1.1.37..." ], [ "Q54D04-1...", "1.1.1.37..." ] ], "headers": [ "uniprotkb_ca...", "enzyme_ec..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "enzyme_ec" }, { "type": "string", "label": "enzyme_activity" } ], [ "Q54D04-1", "1.1.1.37", "(S)-malate + NAD(+) = H(+) + NADH + oxaloacetate." ], [ "Q54D04-1", "1.1.1.37", "" ], [ "Q54D07-1", "7.1.1.8", "a quinol + 2 Fe(III)-[cytochrome c](out) = a quinone + 2 Fe(II)-[cytochrome c](out) + 2 H(+)(out)." ], [ "Q54D07-1", "7.1.1.8", "" ], [ "Q54IM8-1", "1.3.8.-", "" ], [ "Q8MQU6-1", "2.3.3.16", "acetyl-CoA + H2O + oxaloacetate = citrate + CoA + H(+)." ], [ "Q8MQU6-1", "2.3.3.16", "" ], [ "Q869L4-1", "2.7.11.1", "ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein]." ], [ "Q869L4-1", "2.7.11.1", "" ], [ "Q54RX5-1", "4.6.1.16", "pretRNA = a 3'-half-tRNA molecule with a 5'-OH end + a 5'-half-tRNA molecule with a 2',3'-cyclic phosphate end + an intron with a 2',3'-cyclic phosphate and a 5'-hydroxyl terminus." ], [ "Q54RX5-1", "4.6.1.16", "" ], [ "Q557I6-1", "2.3.2.27", "S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine." ], [ "Q557I6-1", "2.3.2.27", "" ], [ "Q54MM7-1", "2.7.7.-", "" ], [ "Q54PT2-1", "3.6.4.6", "ATP + H2O = ADP + H(+) + phosphate." ], [ "Q54PT2-1", "3.6.4.6", "" ], [ "Q54PT3-1", "1.14.-.-", "" ], [ "Q86AX3-1", "4.2.1.49", "4-imidazolone-5-propanoate = H2O + trans-urocanate." ], [ "Q86AX3-1", "4.2.1.49", "" ], [ "Q551E0-1", "3.1.26.11", "Endonucleolytic cleavage of RNA, removing extra 3' nucleotides from tRNA precursor, generating 3' termini of tRNAs. A 3'-hydroxy group is left at the tRNA terminus and a 5'-phosphoryl group is left at the trailer molecule." ], [ "Q551E0-1", "3.1.26.11", "" ], [ "Q54E34-1", "2.7.11.1", "ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein]." ], [ "Q54E34-1", "2.7.11.1", "" ], [ "Q54N47-1", "2.6.1.42", "2-oxoglutarate + L-isoleucine = (S)-3-methyl-2-oxopentanoate + L-glutamate." ], [ "Q54N47-1", "2.6.1.42", "" ], [ "Q54JG7-1", "2.7.11.1", "ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein]." ], [ "Q54JG7-1", "2.7.11.1", "" ], [ "Q86AV6-1", "2.3.3.16", "acetyl-CoA + H2O + oxaloacetate = citrate + CoA + H(+)." ], [ "Q86AV6-1", "2.3.3.16", "" ], [ "Q54N49-1", "5.5.1.4", "D-glucose 6-phosphate = 1D-myo-inositol 3-phosphate." ], [ "Q54N49-1", "5.5.1.4", "" ], [ "Q86KC8-1", "2.4.2.-", "" ], [ "Q54DE8-1", "3.4.23.-", "" ], [ "Q54RJ4-1", "2.7.11.1", "ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein]." ], [ "Q54RJ4-1", "2.7.11.1", "" ], [ "Q54JI5-1", "2.7.4.26", "ATP + isopentenyl phosphate = ADP + isopentenyl diphosphate." ], [ "Q54JI5-1", "2.7.4.26", "" ], [ "Q54JI7-1", "4.3.1.3", "L-histidine = NH4(+) + trans-urocanate." ], [ "Q54JI7-1", "4.3.1.3", "" ], [ "Q54B49-1", "2.3.1.-", "" ], [ "Q54PB4-1", "2.7.11.18", "ATP + L-seryl-[myosin light chain] = ADP + H(+) + O-phospho-L-seryl-[myosin light chain]." ], [ "Q54PB4-1", "2.7.11.18", "" ], [ "Q75JA0-1", "3.6.4.12", "ATP + H2O = ADP + H(+) + phosphate." ], [ "Q75JA0-1", "3.6.4.12", "" ], [ "Q552C6-1", "2.7.12.1", "ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein]." ], [ "Q552C6-1", "2.7.12.1", "" ], [ "Q552C1-1", "2.7.11.1", "ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein]." ], [ "Q552C1-1", "2.7.11.1", "" ], [ "Q75JA4-1", "3.1.3.16", "H2O + O-phospho-L-threonyl-[protein] = L-threonyl-[protein] + phosphate." ], [ "Q75JA4-1", "3.1.3.16", "" ], [ "Q54EP3-1", "3.1.26.5", "Endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor." ], [ "Q54EP3-1", "3.1.26.5", "" ], [ "Q86K86-1", "2.5.1.27", "AMP + dimethylallyl diphosphate = diphosphate + N(6)-(dimethylallyl)adenosine 5'-phosphate." ], [ "Q86K86-1", "2.5.1.27", "" ], [ "Q86A24-1", "2.1.1.-", "" ], [ "Q86A22-1", "1.14.-.-", "" ], [ "P20610-1", "7.1.1.9", "4 Fe(II)-[cytochrome c] + 8 H(+)(in) + O2 = 4 Fe(III)-[cytochrome c] + 4 H(+)(out) + 2 H2O." ], [ "P20610-1", "7.1.1.9", "" ], [ "Q54GG5-1", "2.3.2.26", "S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine." ], [ "Q54GG5-1", "2.3.2.26", "" ], [ "Q8SSY6-1", "2.3.2.26", "S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine." ], [ "Q8SSY6-1", "2.7.11.1", "ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein]." ], [ "P03967-1", "3.6.5.2", "GTP + H2O = GDP + H(+) + phosphate." ], [ "P03967-1", "3.6.5.2", "" ], [ "Q557G1-1", "2.7.11.1", "ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein]." ], [ "Q557G1-1", "2.7.11.1", "" ], [ "P36411-1", "3.6.5.2", "GTP + H2O = GDP + H(+) + phosphate." ], [ "P36411-1", "3.6.5.2", "" ], [ "Q558Z0-1", "6.1.1.19", "ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg)." ], [ "Q558Z0-1", "6.1.1.19", "" ], [ "Q558Z3-1", "3.1.3.16", "H2O + O-phospho-L-threonyl-[protein] = L-threonyl-[protein] + phosphate." ], [ "Q558Z3-1", "3.1.3.16", "" ], [ "Q54KM7-1", "1.4.4.2", "glycine + H(+) + N(6)-[(R)-lipoyl]-L-lysyl-[glycine-cleavage complex H protein] = CO2 + N(6)-[(R)-S(8)-aminomethyldihydrolipoyl]-L-lysyl-[glycine-cleavage complex H protein]." ], [ "Q54KM7-1", "1.4.4.2", "" ], [ "Q54KM0-1", "2.7.7.75", "ATP + H(+) + molybdopterin = adenylyl-molybdopterin + diphosphate." ], [ "Q54KM0-1", "2.10.1.1", "adenylyl-molybdopterin + H(+) + molybdate = AMP + H2O + Mo-molybdopterin." ], [ "B0G138-1", "2.3.1.-", "" ], [ "Q55FI1-1", "2.6.1.19", "2-oxoglutarate + 4-aminobutanoate = L-glutamate + succinate semialdehyde." ], [ "Q55FI1-1", "2.6.1.19", "" ], [ "B0G130-1", "2.3.1.48", "acetyl-CoA + L-lysyl-[histone] = CoA + H(+) + N(6)-acetyl-L-lysyl-[histone]." ], [ "B0G130-1", "2.3.1.48", "" ], [ "B0G133-1", "1.11.1.24", "[thioredoxin]-dithiol + a hydroperoxide = [thioredoxin]-disulfide + an alcohol + H2O." ], [ "B0G133-1", "1.11.1.24", "" ], [ "Q54FC8-1", "2.3.1.-", "" ] ] }, "readme": "Name\n - Dicty Protein Enzyme Annotation (UniProtKB)\n\nVersion\n - v-2.4.1\n\nCreated on\n - \n\nModified on\n - 2024-01-09T04:28:13\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 Enzyme Annotation (UniProtKB) dataset contains dicty [taxid:44689] enzyme annotations for UniProtKB canonical accessions. The dataset contains ec numbers and enzyme activity that describes the enzymatic reactions. 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 - enzyme annotation\n - enzyme\n - UniProtKB\n - enzyme activity\n - EC number\n\n Pipeline Steps\n - Step-1: The script extracts the enzyme 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: uniprot-proteome-dictyostelium-discoideum.nt\n URI: https:/data.glygen.org/ln2downloads/ebi/2024_02_13/uniprot-proteome-dictyostelium-discoideum.nt\n Output Subdomain\n Name: dicty_protein_enzyme_annotation_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/dicty_protein_enzyme_annotation_uniprotkb.csv\n Name: dicty_protein_enzyme_annotation_uniprotkb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/dicty_protein_enzyme_annotation_uniprotkb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"1722\"\n Name: \"enzyme_ec\"\n Description: \"Enzyme Commision number assigned to an enzyme by Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB)\"\n Unique Values: \"720\"\n Name: \"enzyme_activity\"\n Description: \"The catalytic reaction activity of an enzyme in UniProtKB\"\n Unique Values: \"633\"", "downloadurl": "/ln2data/releases/data/v-2.4.1/reviewed/dicty_protein_enzyme_annotation_uniprotkb.csv" }