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

[Stephen Chapman]

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]

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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