A few reactions that look fishy

[johan-gson]

Description of the issue:

• These two reactions are probably the same, but different stoichiometry. They have the same GPR.
  MAR01364, MAR03880:
  arachidonate[c] + O2-[c] => 12-peroxy-(5Z,8Z,10E,14Z)-eicosatetraenoate[c] + H+[c]'
  3 arachidonate[c] + 5 H+[c] + 5 O2-[c] => 3 12-peroxy-(5Z,8Z,10E,14Z)-eicosatetraenoate[c] + 4 H2O[c]'

• These three reactions doesn't make fully sense to me, should probably be investigated:
  MAR03964, MAR07799 and MAR00080

• These two reactions are most likely the same, but with different stoichiometry (same GPR):
  MAR09985, MAR11307:
  5-aminolevulinate[c] + 2 H+[c] <=> 2 H+[s] + 5-aminolevulinate[s]'
  H+[s] + 5-aminolevulinate[s] => 5-aminolevulinate[c] + H+[c]'

Copied from #346

• These reactions could be joined into a reversible rxn to avoid loops, they have the same GPRs:
  'MAR08482': {'3-oxotetradecanoyl-[ACP][c] + H+[c] + NADPH[c] => HMA[c] + NADP+[c]'}
  'MAR02358': {'HMA[c] + NADP+[c] => 3-oxotetradecanoyl-[ACP][c] + H+[c] + NADPH[c]'}

[Devlin-Moyer]

MAR09985 and MAR11307 were addressed in #588/#623
MAR02358 was removed for being a duplicate of MAR08482 in #657
MAR01364, MAR03880, MAR03964, MAR07799 and MAR00080 don't appear to have been mentioned in any other issues or pull requests. I'm not sure I fully understand what's going on in MAR01364 or MAR03880, but I agree with your assessment that they seem to represent the same real-world reaction. MAR03964, MAR07799 and MAR00080 appear to represent V-type ATPases.

[johan-gson]

Nice that you looked into this! I'm thinking we can maybe drop the issue with the ATP hydrolysis functions and close this, or what do you think? They look a bit similar, but could be 3 real reactions. Nice to have someone else in Boston working on this :)

[Devlin-Moyer]

after taking a closer look, MAR03964 seems to be an ATP maintenance reaction rather than a representation of a V-type ATPase (since the proton it produces is still in the cytosol as opposed to the lysosome), and I suspect that MAR07799 is a less accurate version of MAR00080. The GPRs of MAR07799 and MAR00080 involve the same set of genes, but all the genes are just ORed together in the GPR of MAR07799 and grouped into a long nested thing in the GPR of MAR00080 that seems to be representing the existence of alternative isoforms for several subunits of the V-type ATPase complex in humans (source). So there's an argument to be made that MAR07799 should be removed

[Devlin-Moyer]

the arachidonate reactions probably merit a separate issue, because there seem to be several similarly suspicious pairs in addition to the one you mentioned that have the peroxide in a slightly different position, e.g. MAR03882 and MAR01355; MAR03884 and MAR01361

[johan-gson]

Sounds good, I think you know this far better than I do, so just go ahead!