{ "bcoid": "GLY_000855", "title": "Dicty Reactions (Rhea)", "description": "", "filename": "dicty_protein_reactions_rhea.csv", "filetype": "csv", "categories": { "species": [ "Dictyostelium discoideum" ], "molecule": [ "Protein" ], "tag": [ "Reactions Rhea" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "10040...", "..." ], [ "10112...", "..." ] ], "headers": [ "reaction_id...", "reaction_nam..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "reaction_id" }, { "type": "string", "label": "reaction_name" }, { "type": "string", "label": "cellular_location" }, { "type": "string", "label": "pmid" }, { "type": "string", "label": "pathway_id" }, { "type": "string", "label": "equation" }, { "type": "string", "label": "reaction_summary" } ], [ "10040", "", "", "", "", "adenosine 3',5'-bisphosphate + H2O = AMP + phosphate", "" ], [ "10112", "", "", "", "", "L-homocysteine + L-serine = H2O + L,L-cystathionine", "" ], [ "10116", "", "", "", "", "6-phospho-D-gluconate + NADP(+) = CO2 + D-ribulose 5-phosphate + NADPH", "" ], [ "10164", "", "", "", "", "(2R)-2-phosphoglycerate = H2O + phosphoenolpyruvate", "" ], [ "10188", "", "", "", "", "acetoacetyl-CoA + acetyl-CoA + H2O = (3S)-hydroxy-3-methylglutaryl-CoA + CoA + H(+)", "" ], [ "10208", "", "", "", "", "an N-terminal L-alpha-aminoacyl-[protein] + L-arginyl-tRNA(Arg) = H(+) + N-terminal L-arginyl-L-amino acid-[protein] + tRNA(Arg)", "" ], [ "10216", "", "", "", "", "[DNA-directed RNA polymerase] + ATP = ADP + H(+) + phospho-[DNA-directed RNA polymerase]", "" ], [ "10220", "", "", "", "", "ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + H(+) + L-tyrosyl-tRNA(Tyr)", "" ], [ "10224", "", "", "", "", "ATP + pyridoxal = ADP + H(+) + pyridoxal 5'-phosphate", "" ], [ "10244", "", "", "", "", "4-fumarylacetoacetate + H2O = acetoacetate + fumarate + H(+)", "" ], [ "10248", "", "", "", "", "dUTP + H2O = diphosphate + dUMP + H(+)", "" ], [ "10272", "", "", "", "", "a 1,2-diacyl-sn-glycerol + ATP = a 1,2-diacyl-sn-glycero-3-phosphate + ADP + H(+)", "" ], [ "10273", "", "", "", "", "a 1,2-diacyl-sn-glycerol + ATP => a 1,2-diacyl-sn-glycero-3-phosphate + ADP + H(+)", "" ], [ "10276", "", "", "", "", "5-diphospho-1D-myo-inositol 1,2,3,4,6-pentakisphosphate + ATP + H(+) = 1,5-bis(diphospho)-1D-myo-inositol 2,3,4,6-tetrakisphosphate + ADP", "" ], [ "10292", "", "", "", "", "acetyl-CoA + D-glucosamine 6-phosphate = CoA + H(+) + N-acetyl-D-glucosamine 6-phosphate", "" ], [ "10300", "", "", "", "", "D-glyceraldehyde 3-phosphate + NAD(+) + phosphate = (2R)-3-phospho-glyceroyl phosphate + H(+) + NADH", "" ], [ "10336", "", "", "", "", "citrate = D-threo-isocitrate", "" ], [ "10348", "", "", "", "", "5-oxo-L-proline + ATP + 2 H2O = ADP + H(+) + L-glutamate + phosphate", "" ], [ "10380", "", "", "", "", "diphosphate + orotidine 5'-phosphate = 5-phospho-alpha-D-ribose 1-diphosphate + orotate", "" ], [ "10388", "", "", "", "", "GTP + oxaloacetate = CO2 + GDP + phosphoenolpyruvate", "" ], [ "10508", "", "", "", "", "D-glyceraldehyde 3-phosphate + D-sedoheptulose 7-phosphate = aldehydo-D-ribose 5-phosphate + D-xylulose 5-phosphate", "" ], [ "10580", "", "", "", "", "(6S)-5,6,7,8-tetrahydrofolyl-(gamma-L-Glu)(n) + ATP + L-glutamate = (6S)-5,6,7,8-tetrahydrofolyl-(gamma-L-Glu)(n+1) + ADP + H(+) + phosphate", "" ], [ "10596", "", "", "", "", "ATP + L-tyrosyl-[protein] = ADP + H(+) + O-phospho-L-tyrosyl-[protein]", "" ], [ "10684", "", "", "", "", "H2O + O-phospho-L-tyrosyl-[protein] = L-tyrosyl-[protein] + phosphate", "" ], [ "10704", "", "", "", "", "ATP + L-valine + tRNA(Val) = AMP + diphosphate + L-valyl-tRNA(Val)", "" ], [ "10716", "", "", "", "", "D-glucose 6-phosphate = 1D-myo-inositol 3-phosphate", "" ], [ "10736", "", "", "", "", "a primary alcohol + NAD(+) = an aldehyde + H(+) + NADH", "" ], [ "10740", "", "", "", "", "a secondary alcohol + NAD(+) = a ketone + H(+) + NADH", "" ], [ "10748", "", "", "", "", "H(+) + hydrogencarbonate = CO2 + H2O", "" ], [ "10792", "", "", "", "", "5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + H(+) = 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + CO2", "" ], [ "10832", "", "", "", "", "an alpha-D-GlcN-(1->6)-(1,2-diacyl-sn-glycero-3-phospho)-1D-myo-inositol + H2O = 6-(alpha-D-glucosaminyl)-1D-myo-inositol + a 1,2-diacyl-sn-glycero-3-phosphate + H(+)", "" ], [ "10868", "", "", "", "", "a 1,2-diacyl-sn-glycerol + an acyl-CoA = a triacyl-sn-glycerol + CoA", "" ], [ "10980", "", "", "", "", "L-serine = D-serine", "" ], [ "11016", "", "", "", "", "allantoate + H2O = (S)-ureidoglycolate + urea", "" ], [ "11060", "", "", "", "", "ATP + L-isoleucine + tRNA(Ile) = AMP + diphosphate + L-isoleucyl-tRNA(Ile)", "" ], [ "11064", "", "", "", "", "beta-D-fructose 1,6-bisphosphate + H2O = beta-D-fructose 6-phosphate + phosphate", "" ], [ "11068", "", "", "", "", "(5R)-5-O-[alpha-D-glucosyl-(1->2)-beta-D-galactosyl]-5-hydroxy-L-lysyl-[collagen] + H2O = (5R)-5-O-(beta-D-galactosyl)-5-hydroxy-L-lysyl-[collagen] + D-glucose", "" ], [ "11140", "", "", "", "", "alpha-D-mannose 1-phosphate = D-mannose 6-phosphate", "" ], [ "11148", "", "", "", "", "4 Fe(2+) + 4 H(+) + O2 = 4 Fe(3+) + 2 H2O", "" ], [ "11164", "", "", "", "", "a 1,2-diacyl-sn-glycero-3-phosphoethanolamine + S-adenosyl-L-methionine = 1,2-diacyl-sn-glycero-3-phospho-N-methylethanolamine + H(+) + S-adenosyl-L-homocysteine", "" ], [ "11172", "", "", "", "", "(6S)-5-methyl-5,6,7,8-tetrahydrofolate + L-homocysteine = (6S)-5,6,7,8-tetrahydrofolate + L-methionine", "" ], [ "11180", "", "", "", "", "ATP + L-asparagine + tRNA(Asn) = AMP + diphosphate + H(+) + L-asparaginyl-tRNA(Asn)", "" ], [ "11184", "", "", "", "", "3-(carbamoylamino)propanoate + 2 H(+) + H2O = beta-alanine + CO2 + NH4(+)", "" ], [ "11308", "", "", "", "", "acetyl-CoA + ATP + hydrogencarbonate = ADP + H(+) + malonyl-CoA + phosphate", "" ], [ "11332", "", "", "", "", "ATP + RNA(n) = diphosphate + RNA(n)-3'-adenine ribonucleotide", "" ], [ "11356", "", "", "", "", "A + H(+) + NADH = AH2 + NAD(+)", "" ], [ "11436", "", "", "", "", "4 Fe(II)-[cytochrome c] + 8 H(+)(in) + O2 = 4 Fe(III)-[cytochrome c] + 4 H(+)(out) + 2 H2O", "" ], [ "11484", "", "", "", "", "a quinol + 2 Fe(III)-[cytochrome c](out) = a quinone + 2 Fe(II)-[cytochrome c](out) + 2 H(+)(out)", "" ], [ "11488", "", "", "", "", "all-trans-retinol + an acyl-CoA = an all-trans-retinyl ester + CoA", "" ], [ "11489", "", "", "", "", "all-trans-retinol + an acyl-CoA => an all-trans-retinyl ester + CoA", "" ], [ "11580", "", "", "", "", "a CDP-1,2-diacyl-sn-glycerol + myo-inositol = a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol) + CMP + H(+)", "" ], [ "11596", "", "", "", "", "H(+) + orotidine 5'-phosphate = CO2 + UMP", "" ], [ "11600", "", "", "", "", "ATP + CMP = ADP + CDP", "" ], [ "11612", "", "", "", "", "H2O + L-glutamate + NADP(+) = 2-oxoglutarate + H(+) + NADPH + NH4(+)", "" ], [ "11660", "", "", "", "", "a 6-(N-acetyl-alpha-D-glucosaminyl)-1-phosphatidyl-1D-myo-inositol + H2O = acetate + an alpha-D-GlcN-(1->6)-(1,2-diacyl-sn-glycero-3-phospho)-1D-myo-inositol", "" ], [ "11680", "", "", "", "", "ATP + H2O + L-glutamine + XMP = AMP + diphosphate + GMP + 2 H(+) + L-glutamate", "" ], [ "11688", "", "", "", "", "ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu)", "" ], [ "11708", "", "", "", "", "H2O + IMP + NAD(+) = H(+) + NADH + XMP", "" ], [ "11740", "", "", "", "", "2 glutathione + NADP(+) = glutathione disulfide + H(+) + NADPH", "" ], [ "11816", "", "", "", "", "alpha-D-glucose 6-phosphate = beta-D-fructose 6-phosphate", "" ], [ "11888", "", "", "", "", "an aldehyde + H2O + NADP(+) = a carboxylate + 2 H(+) + NADPH", "" ], [ "11920", "", "", "", "", "(4aS,6R)-4a-hydroxy-L-erythro-5,6,7,8-tetrahydrobiopterin = (6R)-L-erythro-6,7-dihydrobiopterin + H2O", "" ], [ "11992", "", "", "", "", "L-pipecolate + O2 = H(+) + H2O2 + L-1-piperideine-6-carboxylate", "" ], [ "12172", "", "", "", "", "alpha-D-glucosamine 6-phosphate + H2O = beta-D-fructose 6-phosphate + NH4(+)", "" ], [ "12188", "", "", "", "", "(R)-N(6)-lipoyl-L-lysyl-[dihydrolipoyllysine-residue succinyltransferase] + 2-oxoglutarate + H(+) = (R)-N(6)-(S(8)-succinyldihydrolipoyl)-L-lysyl-[dihydrolipoyllysine-residue succinyltransferase] + CO2", "" ], [ "12228", "", "", "", "", "ATP + H2O + L-aspartate + L-glutamine = AMP + diphosphate + H(+) + L-asparagine + L-glutamate", "" ], [ "12288", "", "", "", "", "an alpha-L-fucoside + H2O = an alcohol + L-fucose", "" ], [ "12292", "", "", "", "", "ATP + L-serine + tRNA(Ser) = AMP + diphosphate + H(+) + L-seryl-tRNA(Ser)", "" ], [ "12316", "", "", "", "", "a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-3-phosphate) + H2O = a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol) + phosphate", "" ], [ "12356", "", "", "", "", "D-mannose 6-phosphate = D-fructose 6-phosphate", "" ], [ "12452", "", "", "", "", "1D-myo-inositol 3,4,5,6-tetrakisphosphate + ATP = 1D-myo-inositol 1,3,4,5,6-pentakisphosphate + ADP + H(+)", "" ], [ "12460", "", "", "", "", "(S)-malate = fumarate + H2O", "" ], [ "12484", "", "", "", "", "a ribonucleoside 5'-phosphate + H2O = a ribonucleoside + phosphate", "" ], [ "12512", "", "", "", "", "D-aspartate + H2O + O2 = H2O2 + NH4(+) + oxaloacetate", "" ], [ "12540", "", "", "", "", "ATP + L-alanine + tRNA(Ala) = AMP + diphosphate + L-alanyl-tRNA(Ala)", "" ], [ "12556", "", "", "", "", "6-phospho-D-glucono-1,5-lactone + H2O = 6-phospho-D-gluconate + H(+)", "" ], [ "12593", "", "", "", "", "a CDP-1,2-diacyl-sn-glycerol + sn-glycerol 3-phosphate = 1,2-diacyl-sn-glycero-3-phospho-(1'-sn-glycero-3'-phosphate) + CMP + H(+)", "" ], [ "12641", "", "", "", "", "(2R)-3-phosphoglycerate + NAD(+) = 3-phosphooxypyruvate + H(+) + NADH", "" ], [ "12705", "", "", "", "", "[protein]-L-isoaspartate + S-adenosyl-L-methionine = [protein]-L-isoaspartate alpha-methyl ester + S-adenosyl-L-homocysteine", "" ], [ "12709", "", "", "", "", "a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol) + ATP = a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-3-phosphate) + ADP + H(+)", "" ], [ "12721", "", "", "", "", "putrescine + S-adenosyl 3-(methylsulfanyl)propylamine = H(+) + S-methyl-5'-thioadenosine + spermidine", "" ], [ "12733", "", "", "", "", "CO2 + diphosphate + nicotinate beta-D-ribonucleotide = 5-phospho-alpha-D-ribose 1-diphosphate + 2 H(+) + quinolinate", "" ], [ "12789", "", "", "", "", "an alditol + NADP(+) = an aldose + H(+) + NADPH", "" ], [ "12801", "", "", "", "", "ATP + L-seryl-[tau protein] = ADP + H(+) + O-phospho-L-seryl-[tau protein]", "" ] ] }, "readme": "Name\n - Dicty Reactions (Rhea)\n\nVersion\n - v-2.3.1\n\nCreated on\n - \n\nModified on\n - 2024-01-09T05:04:57\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\nDescription Domain\n\n Pipeline Steps\n - Step-1: \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_reactions_rhea.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/dicty_protein_reactions_rhea.csv\n Name: dicty_protein_reactions_rhea.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/dicty_protein_reactions_rhea.stat.csv\n\nFields\n Name: \"reaction_id\"\n Description: \"The identifier assigned to a reaction in Reactome database\"\n Unique Values: \"864\"\n Name: \"reaction_name\"\n Description: \"The name assigned to a reaction in Reactome database\"\n Unique Values: \"1\"\n Name: \"cellular_location\"\n Description: \"The loaction in the cell where reaction occurs\"\n Unique Values: \"1\"\n Name: \"pmid\"\n Description: \"NCBI PubMed database Identifier\"\n Unique Values: \"1\"\n Name: \"pathway_id\"\n Description: \"Pathway Identifier\"\n Unique Values: \"1\"\n Name: \"equation\"\n Description: \"\"\n Unique Values: \"864\"\n Name: \"reaction_summary\"\n Description: \"\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-2.3.1/reviewed/dicty_protein_reactions_rhea.csv" }