reactions r_0533, r_0534, r_0535 appear not balanced

[charamon]

Hi !

I thnk these reactions are not balanced : one should remove the H+ in the right hand side of the reactions r_0533, r_0534 and r_0535.

Best

[edkerk]

Below are the chemical formulas and charges of metabolites involved in r_0534 (hexokinase):

Metabolite	Formula	Charge
ADP[c]	C10H12N5O10P2	-3
ATP[c]	C10H12N5O13P3	-4
D-glucose[c]	C6H12O6	0
D-glucose 6-phosphate[c]	C6H11O9P	-2
H+[c]	H	1

This information can be gathered via e.g.

metIdx = getIndexes(model,{'ADP[c]','ATP[c]','D-glucose[c]','D-glucose 6-phosphate[c]','H+[c]'},'metcomps');
model.metFormulas(metIdx)
model.metCharges(metIdx)

Note that the metabolites are protonated to physiological pH of 7, as is also done in e.g. MetaCyc (in contrast to KEGG). The same holds true for r_0533 and r_0535.

[IndrekM80]

Reaction r_4196 is missing NAD on the other side altogether :)

NADH[erm] + 2 Ferricytochrome b5[erm] <=> H+[erm] + 2 Ferrocytochrome b5[erm]