Difference between KO and ko numbers?

Question

[deep771992chanda]

Hi friends- please forgive me for my silly query. Actually, I was exploring the KEGG pathway database.

1. I could not understand what is the difference between KO and ko IDs? Are they similar or different?
2. Also, is 'module' smaller unit than ko and gives better resolution?
3. Lastly, as I have analyzed some of my data with the MetaCyc database, is there a way I can convert my MetaCyc pathway data into KEGG module/ko data?

Thanks in advance

Answer 1

[andres.firrincieli]

Hello,

I could not understand what is the difference between KO and ko IDs? Are they similar or different?

KO and ko IDs are the same thing

Also, is 'module' smaller unit than ko and gives better resolution?

No. A module is a collection of KO (KEGG orthologs) and therefore RC numbers (Reaction Class identifiers). For example, M00002 includes all the KO and RC involved in the three-carbon compounds reactions of the glycolytic/gluconeogenesis pathway

Lastly, as I have analyzed some of my data with the MetaCyc database, is there a way I can convert my MetaCyc pathway data into KEGG module/ko data?

There are pipelines that build a genome-scale metabolic model by predicting gene-protein-reaction interactions and assigs genes and gene products to databases like KEGG and Metacyc. One example is the RAVEN Toolbox or GPRuler

[deep771992chanda]

Thanks andres. But here it says that

"ko reference pathway highlighting KOs''

So it seems confusing to me. Can you please explain this point mentioned in the KEGG website itself?

1. Clearly, module is smaller unit of pathways. So, is there any difference between pathway and map?

Many Thanks for your response.

[andres.firrincieli]

Hey,

Sorry for the confusion. There are two kind of IDs for pathways in kegg: map and ko. The differences between map and ko is that ko highlights the KOs associated to a given pathway while map does not. Example: map00650 vs ko00650

Clearly, module is smaller unit of pathways. So, is there any difference between pathway and map?

In regard to modules there are no differences between map and ko. Just click on the M00027 GABA (gamma-Aminobutyrate) shunt in map00650 and ko00650

[deep771992chanda]

That's pretty clear now, Andres. Regarding the tools RAVEN ducts to databases like KEGG and Metacyc. One example istoolbox and GPRuler, I think I could not clearly defined my problem to you. Actually, I want to convert the MetaCyc pathway names (or IDs) to KEGG pathway names (or IDs) or vice-versa. Is there any way to do that?

Thanks for your immensely helpful answers.

[andres.firrincieli]

Hey,

I think I could not clearly defined my problem to you. Actually, I want to convert the MetaCyc pathway names (or IDs) to KEGG pathway names (or IDs) or vice-versa. Is there any way to do that?

Sorry, I am not aware of any tool that convert MetaCyc pathway IDs to KEGG pathway IDs. KEGG and MetaCyc are quite different despite reporting the same reactions and compounds. Therefore, the easiest ways to achieve this is to annotate your genome through KEGG and MetaCyc