Questions about gapfill

[Uri David Akavia]

Hello,

I'm trying to run gapfill on a model I modified, and I have some questions.

1) There are some amino acids that appear at least twice in the dictionary file, such as 

ala-L C00041

ala_L C00041

The code in mapKEGGID2Model will not translate C00041 to either, since it has multiple matches. I think that will mean that any gaps with ala_L in my model won't be filled.

Am I right about this?

Should I therefore edit the dictionary file to contain only one match for C00041?

2) There are metabolites that seem very very similar, and I'm not 100% sure what the difference is.

One example is

3hodcoa - (S)-3-Hydroxyoctadecanoyl Coenzyme A versus CE2248 - 3-Hydroxyoctadecanoyl Coenzyme A

Both metabolites exist in RECON3 (for example), but the difference between them seem very small. Are they really different, or is this just two ways to refer to the same metabolite? The KEGG metabolite is called 3-Hydroxyoctadecanoyl Coenzyme A (NO S).

Thanks,

Uri David

[Ronan M.T. Fleming]

Hi Uri,

yes please edit the dictionary file to contain only one match for C00041.

If two metabolites have the same standard InChI then one of them should be deleted, otherwise not. They seem to have two different InChI keys.

WZMAIEGYXCOYSH-FWBOWLIOSA-J
WZMAIEGYXCOYSH-DHAMPVRESA-J

Regards,

Ronan

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Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.
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