questions about MetaCyc pathways

[zj...@cornell.edu]

Hi,

I have used IMG to find MetaCyc pathways associated with my bacterial genomes of interest. I found that sometimes the genomes don't have all the genes for the complete MetaCyc pathway even though MetaCyc marks the genomes as having that pathway. 

For example, MetaCyc says that the Pseudomonas sp. LAIL14HWK12:I1 genome has the β myrcene degradation pathway (PWY-7136). However, this genome has none of the four enzymes of the exact same name involved in this pathway , i.e., linalool dehydratase (EC 4.2.1.127), geraniol isomerase (EC 5.4.4.4), geraniol dehydrogenase (EC 1.1.1.347), or geranial dehydrogenase (EC 1.2.1.86). 

When I used protein BLAST to find if there are orthologs to the geraniol dehydrogenase from Castellaniella defragrans in the above-mentioned Pseudomonas genome, I found several hits, the top one being S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase, although none of the hits have the exact same enzyme name, and have very low identity to the geraniol dehydrogenase from Castellaniella defragrans. I guess this basically means that there is no geraniol dehydrogenase in this Pseudomonas genome. 

So why does IMG MetaCyc function profile mark this genome as having this pathway? Should I trust the results from the MetaCyc function profile?

Thanks a lot,

Zhao