error between chemcial formula of metabolites in a model and as reported by KEGG

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Stephen Chapman

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Apr 21, 2022, 9:49:25 AM4/21/22
to cobra pie
Hi all,

I'm adding reactions to a model and noticed that in the model, the chemical formulas do not match those by kegg. Ill provide an example, eg...

M_cpb_m ; Carbamoyl phosphate, charged formula =                                           
CH2NO5P, charge = -2.


The same metabolite in KEGG, (C00169) has a formula of CH4NO5P, so there is a discrepancy of 2 hydrogens.

Does this difference result from the meaning of 'charged formula' and the two missing hydrogens then result in the charge being -2 ?

Is this standard procedure for reporting formulas?


Dennis van den Berg

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Apr 21, 2022, 11:45:04 AM4/21/22
to Stephen Chapman, cobra pie
Hi Stephen,

Yes, this is the standard way of dealing with compounds. But I think you misread it partially. It is as such:
Name: Carbamoyl phosphate, charged
Formula: CH2NO5P
Charge: -2

So KEGG gives the fully protonated form and most models give the form at pH=7.
So there is no such thing as a 'charged formula' but all compounds should have a formula and a charge.

Hope this helps,

Dennis


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