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!

[edkerk]

@Devlin-Moyer Is this Issue then completely resolved, after #829 ?

[Devlin-Moyer]

#829 takes care of the second item in the original list, but I don't believe the potential redundancy of MAR01364 and MAR03880 has been resolved

[edkerk]

The MAR01364 / MAR03880 item is now resolved. Both are the same GPR-less arachidonate → 12-peroxy-eicosatetraenoate reaction, but MAR01364 (1:1) is charge-imbalanced (reactants −2, products 0) while MAR03880 is balanced, so MAR01364 is removed in #1040.

While checking, the cause turned out to be class-wide, which is the "separate issue" flagged earlier. The simple hydroperoxide fatty acids are each one H short: the formula is CnH30O4 where the correct HPETE/HPDHA anion is CnH31O4 (arachidonate C20H31O2 + O₂ → 12-HPETE C20H31O4 balances exactly). Because of this the clean 1:1 dioxygenations do not balance, and inflated-stoichiometry "workaround" reactions (like MAR03880) were added to force balance around the wrong formula.

Metabolites that need +1 H (CnH30O4 → CnH31O4):

Metabolite	Name	Current → correct
MAM00302	11-peroxy-eicosatetraenoate	C20H30O4 → C20H31O4
MAM00335	12-peroxy-eicosatetraenoate	C20H30O4 → C20H31O4
MAM01214	8-peroxy-eicosatetraenoate	C20H30O4 → C20H31O4
MAM01246	9-peroxy-eicosatetraenoate	C20H30O4 → C20H31O4
MAM00275	10-peroxy-docosahexaenoate	C22H30O4 → C22H31O4
MAM00303	11-peroxy-docosahexaenoate	C22H30O4 → C22H31O4
MAM00372	14-peroxy-docosahexaenoate	C22H30O4 → C22H31O4
MAM00404	16-peroxy-docosahexaenoate	C22H30O4 → C22H31O4
MAM00418	17-peroxy-docosahexaenoate	C22H30O4 → C22H31O4
MAM01198	7-peroxy-docosahexaenoate	C22H30O4 → C22H31O4
MAM01215	8-peroxy-docosahexaenoate	C22H30O4 → C22H31O4

Reactions currently charge-imbalanced because of these formulas (all mass-balanced; charge off by +1 to +4), which would balance once the formulas are corrected:

MAR01355, MAR01358, MAR01361, MAR01363, MAR01405, MAR01410, MAR01411, MAR01412, MAR01413, MAR01414, MAR01416, MAR01417 (plus MAR01364, removed here).

To resolve the class:

1. Correct the 11 hydroperoxide formulas above (CnH30O4 → CnH31O4).
2. The reactions above then balance as parent + O₂ → hydroperoxide.
3. The inflated-stoichiometry duplicates (MAR03880, MAR03882, MAR03884, …) become redundant and can be replaced by the clean 1:1 form.
4. Several of these reactions use superoxide (O2-, MAM02631) where molecular O₂ (MAM02630) is the actual lipoxygenase co-substrate; those should be switched to O₂.