[BUG] KEGG Module annotations arn't exist in KEGG database

[GuyTadmor-28]

Hi,

I am using eggNOG-mapper (v.2.1.12) to annotate some genes predicted from metagenomic data, and it seems like many of the associated KEGG modules aren't in the KEGG db (for example, if you look for 'M00260' in KEGG modules, you get 'NO ENTRY FOUND.').

After consulting with some of my colleagues, they encounter the same issue.

Any idea for a solution?

Thanks!

[JeffreyDeanBrown]

This is an interesting issue, it appears that there are more than one publication online referencing "M00260" as "DNA polymerase III complex, bacteria"- but the KEGG database does not seem to have it. Perhaps there was an update to KEGG at some point? I'll keep poking around out of curiosity, but it doesn't seem to be specific to eggnog as others have referenced this missing module.

[JeffreyDeanBrown]

It looks like the KEGG module database was update late 2019 in release 92 KEGG release notes where they removed some redundancies and reorganized. eggnog 5.0 was published late 2018, so the current eggnog.db might not reflect the new modules. To confirm we would need to get access to the pre-2019 module database and check the eggnog.db using an sqlite utility. I might have time to check this out within the next week or so.

In the meantime, you can copy your KO numbers to a text file and run them through KEGG's mapping tools, specifically the reconstruct tool. That should at least give you current module ID numbers for your data. The reconstruct tool has info for formatting your text file. eggnog exports KO numbers with a prefix (i.e. ko:K######), you will need to remove the "ko:" and just keep the K######. Excel can do this, or you can make a quick script to do it as well

[GuyTadmor-28]

Hi Jeffrey,

Thank you for the quick response! Indeed, the reconstruction tool solves the problem. For the sake of other users who might read this, I should note that I did lose most of the annotations during the reconstruction, although I believe this is due to the current KEGG annotation and not an issue with eggNOG.

Thanks again!

[JeffreyDeanBrown]

No problem :) I couldn't find any way to access previous versions of KEGG or KEGG modules, but others with more experience might know how to do so. I don't know if there is currently a way to reference old versions of KEGG modules to confirm my suspicions, or to convert old modules to newer ones beyond re-using ko-numbers in more current KEGG tools.