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@larsgw/gpml-rhea

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Annotate GPML pathways with Rhea identifiers

github.com/larsgw/gpml-rhea

larsgw/gpml-rhea

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# GPML-Rhea Collect chemical reactions from a GPML file and look for matching Rhea equations. Requires: - MIM interactions compatible with https://github.com/BiGCAT-UM/WikiPathwaysInteractions/tree/master/FilesGPML#readme - Metabolites with ChEBI identifiers ## Install npm install --global @larsgw/gpml-rhea ## Usage GPML-Rhea gpml-rhea [file] Read file gpml-rhea - Read from standard in gpml-rhea -v, --version Get the version gpml-rhea -h, --help Print this message ## Example > curl -L -o pathway.gpml https://webservice.wikipathways.org/getPathwayAs?fileType=gpml&pwId=WP5019&revision=113587 > gpml-rhea pathway.gpml id192c7b4a: 5,10-Methenyltetrahydrofolate + NADH → 5,10-Methylenetetrahydrofolate + NAD(1-) --------------------------------------------- Rhea: 0 results --------------------------------------------- id4f3af248: Oxidised ferredoxin → Reduced ferredoxin --------------------------------------------- Rhea: 0 results --------------------------------------------- id59fbd0e3: 10-Formyltetrahydrofolate + dihydrogen → 5,10-Methenyltetrahydrofolate --------------------------------------------- Rhea: 0 results --------------------------------------------- id8e976caf: 5-Methyltetrahydrofolate → methyl + Tetrahydrofolate --------------------------------------------- Rhea: 0 results --------------------------------------------- idb70e2922: NAD(1-) → NADH --------------------------------------------- Rhea: 0 results --------------------------------------------- idcb0cc195: formate + ATP + Tetrahydrofolate → 10-Formyltetrahydrofolate + hydrogenphosphate + ADP --------------------------------------------- Rhea: 0 results --------------------------------------------- ide2e37f0: 5,10-Methylenetetrahydrofolate + NADH → 5-Methyltetrahydrofolate + NAD(1-) --------------------------------------------- Rhea: 0 results --------------------------------------------- ideb932d04: carbon monooxide + HSCoA + methyl → acetyl-CoA --------------------------------------------- Rhea: 0 results --------------------------------------------- idee9950c3: carbon dioxide + dihydrogen → formate + hydron --------------------------------------------- Rhea: 1 results 27610: formate + H(+) = CO2 + H2 --------------------------------------------- idf6f6d75: dihydrogen → hydron --------------------------------------------- Rhea: 13 results 24636: H2 + NAD(+) = H(+) + NADH 27610: formate + H(+) = CO2 + H2 29047: a menaquinone + 2 H(+)(in) + H2 = a menaquinol + 2 H(+)(out) 29051: 2 H(+)(in) + H2 + menaquinone-8 = 2 H(+)(out) + menaquinol-8 29055: a ubiquinone + 2 H(+)(in) + H2 = a ubiquinol + 2 H(+)(out) 29059: 2 H(+)(in) + H2 + ubiquinone-8 = 2 H(+)(out) + ubiquinol-8 30279: 2 H2 + NAD(+) + 2 oxidized [2Fe-2S]-[ferredoxin] = 3 H(+) + NADH + 2 reduced [2Fe-2S]-[ferredoxin] 35591: H2 + n sulfur = H(+) + hydrogen sulfide + (n-1) sulfur 17445: H2 + 2 oxidized [2Fe-2S]-[ferredoxin] = 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] 18637: H2 + NADP(+) = H(+) + NADPH 20017: 5,10-methenyl-5,6,7,8-tetrahydromethanopterin + H2 = 5,10-methylenetetrahydromethanopterin + H(+) 20625: 2 [Fe(III)-cytochrome c3] + H2 = 2 [Fe(II)-cytochrome c3] + 2 H(+) 55748: coenzyme B + coenzyme M + 2 H(+) + 2 reduced [2Fe-2S]-[ferredoxin] = coenzyme M-coenzyme B heterodisulfide + 2 H2 + 2 oxidized [2Fe-2S]-[ferredoxin] ---------------------------------------------