Question: Annotate unknown reaction from known reactants
0
gravatar for Miche
4.0 years ago by
Miche0
Australia Brisbane
Miche0 wrote:

Hi all,

Apologies if this is a repeated question.

I have an annotated genome (RAST) but I am missing some reactions. The bacterium I am studying degrades a known toxin to unknown compoundss, but this pathway is not present in the annotation.

KEGG’s PathPred starting from a similar compound returned 50s of possible reactions. Now, how to search in my genome for those reactions and possibly list similarities?

Is there any other way to annotate a unknown degradation pathways?

Thanks in advance. 

Miche

ADD COMMENTlink modified 12 weeks ago by Biostar ♦♦ 20 • written 4.0 years ago by Miche0
1

It has been a while working with KEGG. I can remember, that for each biochemical catalysed reaction, KEGG linked the E.C. number which is closely related to KEGG's ontology.

Thus, I'd check if any of the reactions paths' enzymes are annotated as genes in your species or if the genes can be linked via the ontology.

ADD REPLYlink written 12 weeks ago by michael.ante3.2k
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