Closed sjm41 closed 2 months ago
pgaudet
commented
3 months ago We should also look at phosphoenolpyruvate carboxylase activity when lookin at this group. phosphoenolpyruvate carboxylase activity seems to be under the wrong parent (=phosphoenolpyruvate carboxykinase activity)
rozaru
commented
2 months ago Not sure about this but as the malate reaction is the predominante one could
xref: EC:1.1.1.40 -> make ExactMatch
in
id: GO:0004473 name: malate dehydrogenase (decarboxylating) (NADP+) activity def: "Catalysis of the reaction: (S)-malate + NADP+ = pyruvate + CO2 + NADPH + H+." [EC:1.1.1.40] xref: EC:1.1.1.40 xref: RHEA:18253
xref: EC:1.1.1.40 -> make broadMatch
and
xref: EC:1.1.1.38 -> make ExactMatch
in
id: GO:0004471 name: malate dehydrogenase (decarboxylating) (NAD+) activity def: "Catalysis of the reaction: (S)-malate + NAD+ = pyruvate + CO2 + NADH + H+." [EC:1.1.1.38, EC:1.1.1.39] xref: EC:1.1.1.38 xref: EC:1.1.1.39 xref: RHEA:12653
xref: EC:1.1.1.38 -> make broadMatch xref: EC:1.1.1.39 & xref: RHEA:12653 -> make exactMatch Replace def xref with RHEA:12653
Looking at these ECs (following on from #28243):
EC:1.1.1.38 malate dehydrogenase (oxaloacetate-decarboxylating) (S)-malate + NAD(+) <=> CO2 + NADH + pyruvate H(+) + oxaloacetate <=> CO2 + pyruvate
EC 1.1.1.39 malate dehydrogenase (decarboxylating) (S)-malate + NAD(+) <=> CO2 + NADH + pyruvate
EC:1.1.1.40 malate dehydrogenase (oxaloacetate-decarboxylating) (NADP(+)) (S)-malate + NADP(+) <=> CO2 + NADPH + pyruvate H(+) + oxaloacetate <=> CO2 + pyruvate
EC:4.1.1.112 oxaloacetate decarboxylase H(+) + oxaloacetate <=> CO2 + pyruvate
They are term/def xrefs on the following 3 GO terms - I've suggested what needs to be done to make the relationships clearer. Let me know if you agree @pgaudet (this issue is on the #26235 list/spreadsheet, marked as 'to discuss')
id: GO:0008948 name: oxaloacetate decarboxylase activity def: "Catalysis of the reaction: oxaloacetate = pyruvate + CO2." [EC:1.1.1.38, EC:1.1.1.40, EC:4.1.1.112] xref: EC:1.1.1.38 xref: EC:1.1.1.40 xref: EC:4.1.1.112 xref: RHEA:15641
id: GO:0004471 name: malate dehydrogenase (decarboxylating) (NAD+) activity def: "Catalysis of the reaction: (S)-malate + NAD+ = pyruvate + CO2 + NADH + H+." [EC:1.1.1.38, EC:1.1.1.39] xref: EC:1.1.1.38 xref: EC:1.1.1.39 xref: RHEA:12653
id: GO:0004473 name: malate dehydrogenase (decarboxylating) (NADP+) activity def: "Catalysis of the reaction: (S)-malate + NADP+ = pyruvate + CO2 + NADPH + H+." [EC:1.1.1.40] xref: EC:1.1.1.40 xref: RHEA:18253