Unbalance reactions checked in the new content of Human-GEM

[JHL-452b]

Current behavior:

With the curation of Human-GEM, there are some unbalance rxns here that did not exist in the previous model.

ID	Reaction	Cause of imbalance	changing source
MAR01444	ATP + H+ + H2O + K+ + 2 Na+ --> ADP + H+ + K+ + 2 Na+ + Pi	{'charge': -1, 'H': -1}	#581
MAR20005	H2O + NAD+ + 20-oxo-(5Z,8Z,11Z,14Z)-eicosatetraenoate --> 2 H+ + NADH + (5Z,8Z,11Z,14Z)-eicosatetraenedioate	{'charge': 1}	addRxnGly_20230414.tsv
MAR20006	H2O + NAD+ + 20-oxo-(5Z,8Z,11Z,14Z)-eicosatetraenoate --> 2 H+ + NADH + (5Z,8Z,11Z,14Z)-eicosatetraenedioate	{'charge': 1}	addRxnGly_20230414.tsv
MAR20007	10-HETE + NAD+ --> H+ + NADH + 20-oxo-(5Z,8Z,11Z,14Z)-eicosatetraenoate	{'charge': 1}	addRxnGly_20230414.tsv
MAR20008	10-HETE + NAD+ --> H+ + NADH + 20-oxo-(5Z,8Z,11Z,14Z)-eicosatetraenoate	{'charge': 1}	addRxnGly_20230414.tsv
MAR20021	mead acid + O2 + FMNH2 --> FMN + H+ + H2O + 19-hydroxy-(5Z,8Z,11Z)-eicosatrienoate	{'charge': 2, 'H': 1}	addRxnGly_20230414.tsv
MAR20022	mead acid + O2 + FMNH2 --> FMN + H+ + H2O + 19-hydroxy-(5Z,8Z,11Z)-eicosatrienoate	{'charge': 2, 'H': 1}	addRxnGly_20230414.tsv
MAR20023	EPA + O2 + FMNH2 --> FMN + H+ + H2O + 19-hydroxy-(5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate	{'charge': 2, 'H': 1}	addRxnGly_20230414.tsv
MAR20024	EPA + O2 + FMNH2 --> FMN + H+ + H2O + 19-hydroxy-(5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate	{'charge': 2, 'H': 1}	addRxnGly_20230414.tsv
MAR20025	DHA + O2 + FMNH2 --> FMN + H+ + H2O + 21-hydroxy-(4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoate	{'charge': 2, 'H': 1}	addRxnGly_20230414.tsv
MAR20026	DHA + O2 + FMNH2 --> FMN + H+ + H2O + 21-hydroxy-(4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoate	{'charge': 2, 'H': 1}	addRxnGly_20230414.tsv
MAR20027	lauric acid + O2 + FMNH2 --> FMN + H+ + H2O + 11-hydroxydodecanoate	{'charge': 2, 'H': 1}	addRxnGly_20230414.tsv
MAR20028	lauric acid + O2 + FMNH2 --> FMN + H+ + H2O + 11-hydroxydodecanoate	{'charge': 2, 'H': 1}	addRxnGly_20230414.tsv
MAR20029	myristic acid + O2 + FMNH2 --> FMN + H+ + H2O + 13-hydroxytetradecanoate	{'charge': 2, 'H': 1}	addRxnGly_20230414.tsv
MAR20030	myristic acid + O2 + FMNH2 --> FMN + H+ + H2O + 13-hydroxytetradecanoate	{'charge': 2, 'H': 1}	addRxnGly_20230414.tsv
MAR20046	H2O + hexadecenal + NAD+ --> 2 H+ + NADH + (E)-hexadec-2-enoate	{'charge': 1}	addRxnGly_20230414.tsv
MAR20047	H2O + hexadecenal + NAD+ --> 2 H+ + NADH + (E)-hexadec-2-enoate	{'charge': 1}	addRxnGly_20230414.tsv
MAR20049	H2O + NAD+ + 22-oxodocosanoate --> 2 H+ + NADH + Docosanedioicacid	{'charge': -1}	addRxnGly_20230414.tsv
MAR20050	H2O + NAD+ + 22-oxodocosanoate --> 2 H+ + NADH + Docosanedioicacid	{'charge': -1}	addRxnGly_20230414.tsv
MAR20064	2-trans,6-trans-farnesal + H2O + NAD+ --> 2 H+ + NADH + (2E,6E)-farnesoate	{'charge': 1}	addRxnGly_20230414.tsv
MAR20065	2-trans,6-trans-farnesal + H2O + NAD+ --> 2 H+ + NADH + (2E,6E)-farnesoate	{'charge': 1}	addRxnGly_20230414.tsv
MAR20098	farnesyl-PP + 5 isopentenyl-pPP --> dehydrodolichol-diphosphate + 5 PPi	{'C': 60, 'H': 96}	addRxnAA_20230518.tsv
MAR20111	acetyl-CoA + glyoxalate + H2O --> CoA + malate	{'charge': -1, 'H': -1}	commits
MAR20112	apoC-lys_btn + ATP + HCO3- --> ADP + H+ + Pi	{'charge': 1, 'C': -17, 'H': -26, 'N': -4, 'O': -5, 'S': -1, 'X': -1}	#624

Proposed changes:

rxn_id	rxn_eq	change	check balance
MAR01444	MAM01371c + MAM02039e + MAM02040c + MAM02200e + 2 MAM02519c --> MAM01285c + MAM02039c + MAM02200c + 2 MAM02519e + MAM02751c	remove H+(MAM02039e):-1	TRUE
MAR20005	MAM02040n + MAM02552n + MAM20003n --> 2 MAM02039n + MAM02553n + MAM20004n	change charge of MAM20004n to -1	TRUE
MAR20006	MAM02040c + MAM02552c + MAM20005c --> 2 MAM02039c + MAM02553c + MAM20006c	change charge of MAM20006c to -1	TRUE
MAR20007	MAM00270n + MAM02552n --> MAM02039n + MAM02553n + MAM20003n	change charge of MAM20004n to -1	TRUE
MAR20021	MAM02457r + MAM02630r + MAM20019r --> MAM01828r + MAM02039r + MAM02040r + MAM20018r	remove H+(MAM02039r):1; change charge of MAM20018r to -1	TRUE
MAR20022	MAM02457i + MAM02630i + MAM20019i --> MAM01828i + MAM02039i + MAM02040i + MAM20021i	remove H+(MAM02039i):1; change charge of MAM20021i to -1	TRUE
MAR20023	MAM01784r + MAM02630r + MAM20019r --> MAM01828r + MAM02039r + MAM02040r + MAM20024r	remove H+(MAM02039r):1; change charge of MAM20024r to -1	TRUE
MAR20024	MAM01784i + MAM02630i + MAM20019i --> MAM01828i + MAM02039i + MAM02040i + MAM20025i	remove H+(MAM02039i):1; change charge of MAM20025i to -1	TRUE
MAR20025	MAM01689r + MAM02630r + MAM20019r --> MAM01828r + MAM02039r + MAM02040r + MAM20026r	remove H+(MAM02039r):1; change charge of MAM20026r to -1	TRUE
MAR20026	MAM01689i + MAM02630i + MAM20019i --> MAM01828i + MAM02039i + MAM02040i + MAM20027i	remove H+(MAM02039i):1; change charge of MAM20027i to -1	TRUE
MAR20027	MAM02344r + MAM02630r + MAM20019r --> MAM01828r + MAM02039r + MAM02040r + MAM20028r	remove H+(MAM02039r):1; change charge of MAM20028r to -1	TRUE
MAR20028	MAM02344i + MAM02630i + MAM20019i --> MAM01828i + MAM02039i + MAM02040i + MAM20029i	remove H+(MAM02039i):1; change charge of MAM20029i to -1	TRUE
MAR20029	MAM02494r + MAM02630r + MAM20019r --> MAM01828r + MAM02039r + MAM02040r + MAM20030r	remove H+(MAM02039r):1; change charge of MAM20030r to -1	TRUE
MAR20030	MAM02494i + MAM02630i + MAM20019i --> MAM01828i + MAM02039i + MAM02040i + MAM20031i	remove H+(MAM02039i):1; change charge of MAM20031i to -1	TRUE
MAR20046	MAM02040r + MAM02116r + MAM02552r --> 2 MAM02039r + MAM02553r + MAM20041r	change charge of MAM20041r to -1	TRUE
MAR20047	MAM02040c + MAM02116c + MAM02552c --> 2 MAM02039c + MAM02553c + MAM20042c	change charge of MAM20042c to -1	TRUE
MAR20049	MAM02040r + MAM02552r + MAM20043r --> 2 MAM02039r + MAM02553r + MAM03560r	change charge of MAM20043r to -1	TRUE
MAR20050	MAM02040c + MAM02552c + MAM20044c --> 2 MAM02039c + MAM02553c + MAM03560c	change charge of MAM20044c to -1	TRUE
MAR20064	MAM00677r + MAM02040r + MAM02552r --> 2 MAM02039r + MAM02553r + MAM20056r	change charge of MAM20056r to -1	TRUE
MAR20065	MAM00677c + MAM02040c + MAM02552c --> 2 MAM02039c + MAM02553c + MAM20057c	change charge of MAM20057c to -1	TRUE
MAR20098	MAM01806r + 5 MAM02187r --> MAM01657r + 5 MAM02759r	change formula of MAM01657r to 'C40H65O7P2'	TRUE
MAR20111	MAM01261m + MAM02007m + MAM02040m --> MAM01597m + MAM02439m	add H+(MAM02039m):1	TRUE
MAR20112	MAM01357m + MAM01371m + MAM02046m --> MAM01285m + MAM02039m + MAM02751m	add MAM01422m(1) as productant	TRUE

All these changes ensure that the current reaction is balanced without affecting other reactions.

[JHL-452b]

@Devlin-Moyer I noticed that you have added MAR20111 and MAR20112. Could you please help me to check whether the above modifications are OK?

[JonathanRob]

Really nice work @JHL-452b, thank you for this!

[Devlin-Moyer]

If by "remove H+(MAM02039m):1" you mean "add one H⁺ (MAM02039m) to MAR20111 as a product", then yes, both of your proposed fixes for MAR20111 and MAR20112 make sense to me; sorry for missing those errors when I created them.

[JHL-452b]

If by "remove H+(MAM02039m):1" you mean "add one H+ (MAM02039m) to MAR20111 as a product"

Yeah, it's a mistake in my statement, which has been corrected.

[JHL-452b]

In Human-GEM version 1.18, the above reactions were modified to make the model consistent, but the additional unbalanced reactions in the current develop branch still make the model inconsistent. Thus, I try to find and resolve the following imbalance reactions so that the model regains consistency.

ID	Reaction	Cause of imbalance	changing source	balance plan	check balance
MAR03481	MAM01371c + 2.0 MAM02040c + MAM02747c <=> MAM01285c + MAM01597c + MAM02039c + MAM02746x + MAM02751c	{'charge': -1.0, 'H': -1.0}	#805	add additional H+(MAM02039c) as a product	True
MAR20177	MAM02393m + MAM20081m --> MAM02984m + MAM20082m	{'C': -11.0, 'H': -23.0, 'N': -1.0, 'O': -2.0, 'S': -2.0}	#753	replace the formula of MAM20082m from None to C11H23N1O2S2	True

[Devlin-Moyer]

Am I missing something or does PR #815 not mention MAR03481?

[Devlin-Moyer]

ah I see you meant #805; both of your proposed changes to fix the mass balance issues with those reactions look good to me

[JHL-452b]

Am I missing something or does PR #815 not mention MAR03481?

Yeah, it's a wrong link and I corrected it.

So, all these reactions has been modified and I will go head.