Fix/fmn fmnh2 ids

[Devlin-Moyer]

Main improvements in this PR:

As proposed in #711:

• Changes the ID of MAM20020r to MAM01828r to match FMN metabolites in other compartments
• Changes the ID of MAM20023i to MAM01828i to match FMN metabolites in other compartments
• Changes the ID of MAM20022i to MAM20019i to match FMNH2 metabolites in other compartments
• Changes the formulas of MAM01828r and MAM01828i to C17H19N4O9P
• Associates MAM01828r and MAM01828i with KEGG ID C00061
• Associates MAM20019r and MAM20019i with KEGG ID C01847

I hereby confirm that I have:

• Tested my code on my own computer for running the model
• Selected develop as a target branch
• Any removed reactions and metabolites have been moved to the corresponding deprecated identifier lists

[haowang-bioinfo]

these mets were from this table that can be traced back to #535. It appears that large changes are prone to introducing errors

please also move MAM20020r, MAM20023i, MAM20022i to deprecatedMetabolites.tsv

[haowang-bioinfo]

the charge state of FMN (MAM01828) should all be changed to -3, according to CHEBI annotation under pH=7.3

[Devlin-Moyer]

oh I just edited the rows for MAM20020r, MAM20023i, and MAM20022i in metabolites.tsv directly to change the IDs rather than moving them to deprecatedMetabolites.tsv and making new rows for the new IDs in metabolites.tsv; do you want me to make new rows in deprecatedMetabolites.tsv for them?

Also if we change the charges on any of the FMN metabolites, we're going to have to edit all the reactions they participate in to make sure they're still charge- and mass-balanced

[haowang-bioinfo]

do you want me to make new rows in deprecatedMetabolites.tsv for them?

yes please, these ids won't be reused anyway

Also if we change the charges on any of the FMN metabolites, we're going to have to edit all the reactions they participate in to make sure they're still charge- and mass-balanced

you are right, the related reactions should be balanced. Please double check, maybe they already are

[Devlin-Moyer]

I haven't looked at all of these super carefully, but I'm pretty sure every single one would have to be changed to keep them charge-balanced after changing the charges on the FMN metabolites from -2 to -3
(the number in parentheses after the compartment in square brackets is the charge on the preceding metabolite)

ID	Reaction	Balanced? (Total Charge)
MAR06509	FAD [c] (-2) + H2O [c] (0) --> AMP [c] (-2) + FMN [c] (-2) + 2 H+ [c] (1)	yes (-2)
MAR20122	ADP [x] (-3) + FMN [c] (-2) <=> ADP [c] (-3) + FMN [x] (-2)	N/A (transport)
MAR20120	FMN [c] (-2) + NAD+ [x] (-1) <=> FMN [x] (-2) + NAD+ [c] (-1)	N/A (transport)
MAR06508	ATP [c] (-4) + FMN [c] (-2) + H+ [c] (1) --> FAD [c] (-2) + PPi [c] (-3)	yes (-5)
MAR06506	ATP [c] (-4) + riboflavin [c] (0) --> ADP [c] (-3) + FMN [c] (-2) + H+ [c] (1)	yes (-4)
MAR06507	FMN [c] (-2) + H2O [c] (0) --> Pi [c] (-2) + riboflavin [c] (0)	yes (-2)
MAR20119	FAD [x] (-2) + FMN [c] (-2) <=> FAD [c] (-2) + FMN [x] (-2)	N/A (transport)
MAR20121	AMP [x] (-2) + FMN [c] (-2) <=> AMP [c] (-2) + FMN [x] (-2)	N/A (transport)
MAR20118	CoA [x] (-4) + FMN [c] (-2) <=> CoA [c] (-4) + FMN [x] (-2)	N/A (transport)
MAR20117	FAD [x] (-2) + H2O [x] (0) --> AMP [x] (-2) + FMN [x] (-2) + 2 H+ [x] (1)	yes (-2)
MAR08962	FMN [e] (-2) <=>	N/A (exchange)
MAR08969	FMN [e] (-2) + H2O [e] (0) --> Pi [e] (-2) + riboflavin [e] (0)	yes (-2)
MAR08968	FAD [e] (-2) + H2O [e] (0) --> AMP [e] (-2) + FMN [e] (-2) + 2 H+ [e] (1)	yes (-2)
MAR20027	lauric acid [r] (-1) + O2 [r] (0) + FMNH2 [r] (-2) --> FMN [r] (-2) + H+ [r] (1) + H2O [r] (0) + 11-hydroxydodecanoate [r] (0)	no (-3, -1)
MAR20023	EPA [r] (-1) + O2 [r] (0) + FMNH2 [r] (-2) --> FMN [r] (-2) + H+ [r] (1) + H2O [r] (0) + 19-hydroxy-(5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate [r] (0)	no (-3, -1)
MAR20025	DHA [r] (-1) + O2 [r] (0) + FMNH2 [r] (-2) --> FMN [r] (-2) + H+ [r] (1) + H2O [r] (0) + 21-hydroxy-(4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoate [r] (0)	no (-3, -1)
MAR20021	mead acid [r] (-1) + O2 [r] (0) + FMNH2 [r] (-2) --> FMN [r] (-2) + H+ [r] (1) + H2O [r] (0) + 19-hydroxy-(5Z,8Z,11Z)-eicosatrienoate [r] (0)	no (-3, -1)
MAR20029	myristic acid [r] (-1) + O2 [r] (0) + FMNH2 [r] (-2) --> FMN [r] (-2) + H+ [r] (1) + H2O [r] (0) + 13-hydroxytetradecanoate [r] (0)	no (-3, -1)
MAR20026	DHA [i] (-1) + O2 [i] (0) + FMNH2 [i] (-2) --> FMN [i] (-2) + H+ [i] (1) + H2O [i] (0) + 21-hydroxy-(4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoate [i] (0)	no (-3, -1)
MAR20028	lauric acid [i] (-1) + O2 [i] (0) + FMNH2 [i] (-2) --> FMN [i] (-2) + H+ [i] (1) + H2O [i] (0) + 11-hydroxydodecanoate [i] (0)	no (-3, -1)
MAR20022	mead acid [i] (-1) + O2 [i] (0) + FMNH2 [i] (-2) --> FMN [i] (-2) + H+ [i] (1) + H2O [i] (0) + 19-hydroxy-(5Z,8Z,11Z)-eicosatrienoate [i] (0)	no (-3, -1)
MAR20030	myristic acid [i] (-1) + O2 [i] (0) + FMNH2 [i] (-2) --> FMN [i] (-2) + H+ [i] (1) + H2O [i] (0) + 13-hydroxytetradecanoate [i] (0)	no (-3, -1)
MAR20024	EPA [i] (-1) + O2 [i] (0) + FMNH2 [i] (-2) --> FMN [i] (-2) + H+ [i] (1) + H2O [i] (0) + 19-hydroxy-(5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate [i] (0)	no (-3, -1)

[Devlin-Moyer]

hmm it looks like all of the reactions that involve MAM01828r are already charge-imbalanced (-3 on the left and -1 on the right), but just changing the charge on FMN to -3 would still leave it at -3 vs -2

[Devlin-Moyer]

oh it occurs to me that part of the problem with the currently-imbalanced reactions in [i] and [r] is that they have (neutral) fatty acids as reactants and produce the conjugate bases + protons as products, but the conjugate bases incorrectly have charges of 0. While changing all of those charges to -1 would I think be more realistic, we'd have to see if all of the other reactions each of those metabolites participates in would also have to be adjusted, and I don't know how many more rounds of that would be necessary

[haowang-bioinfo]

hmm it looks like all of the reactions that involve MAM01828r are already charge-imbalanced (-3 on the left and -1 on the right), but just changing the charge on FMN to -3 would still leave it at -3 vs -2

right, maybe okay to merge and resolve the balancing issue another time

[haowang-bioinfo]

now the issues mentioned in #711 have been addressed