Ammonia/Ammonium Duplicate Reactions

[Devlin-Moyer]

The Problem:

There are several reactions that are completely identical except one uses NH₄⁺ (MAM02579) and the other uses NH₃ (MAM02578) + H⁺:

ID	Reaction	Genes
MAR01515	H2O + methylamine + O2 --> formaldehyde + H2O2 + NH4+	AOC1 or AOC3 or AOC2
MAR08529	H2O + methylamine + O2 --> formaldehyde + H+ + H2O2 + NH3	AOC1 or AOC3 or AOC2
MAR00039	1,3-diaminopropane + H2O + O2 --> 3-amino-propanal + H2O2 + NH4+	AOC1 or AOC3 or AOC2
MAR07992	1,3-diaminopropane + H2O + O2 --> 3-amino-propanal + H+ + H2O2 + NH3	AOC1 or AOC3 or AOC2
MAR00096	3-ureidoisobutyrate + 2 H+ + H2O --> CO2 + D-3-amino-isobutanoate + NH4+	UPB1
MAR04819	3-ureidoisobutyrate + H+ + H2O --> CO2 + D-3-amino-isobutanoate + NH3	UPB1
MAR02027	cysteine + H2O <=> H+ + H2S + NH4+ + pyruvate	CTH
MAR04302	cysteine + H2O --> 2 H+ + H2S + NH3 + pyruvate	CTH
MAR02006	2 ATP + CO2 + H2O + NH4+ --> 2 ADP + carbamoyl-phosphate + 3 H+ + Pi	CPS1
MAR03873	2 ATP + CO2 + H2O + NH3 --> 2 ADP + carbamoyl-phosphate + 2 H+ + Pi	CPS1

Uniprot lists all reactions associated with AOC1, AOC2, AOC3, UPB1, CTH, and/or CPS1 with NH₄⁺ rather than NH₃.

Proposed Changes:

Since MAR02027 (NH₄⁺) is reversible but MAR04302 (NH₃) is irreversible, Uniprot says that reaction should be irreversible, most similar reactions already in Human-GEM involve NH₃ (MAM02578) rather than NH₄⁺ (MAM02579), I think it makes sense to remove all of the NH₄⁺ versions and keep all of the NH₃ versions. MAR05127: NH4+ [c] ⇔ H+ [c] + NH3 [c] allows ammonium and ammonia to freely interconvert (which is reasonable; that reaction is spontaneous in aqueous solutions), so it's not really contradicting Uniprot to keep the NH₃ versions instead of the NH₄⁺ versions, and that would make the proposed changes a little simpler:

• [x] Remove MAR01515 for being a duplicate of MAR08529
• [x] Remove MAR00039 for being a duplicate of MAR07992
• [x] Remove MAR00096 for being a duplicate of MAR04819
• [x] Remove MAR02027 for being a duplicate of MAR04302
• [x] Remove MAR02006 for being a duplicate of MAR03873
• [x] Merge annotations/references/etc. from removed reactions into corresponding kept reactions

[feiranl]

Agree! please go ahead and make these changes!

[Devlin-Moyer]

Fixed in #677