Mapping KOs to Uniref90 in humann3

Microbial community profiling HUMAnN
1

Dear developers and users,

I would like to annotate the KEGG Orthogroups (KOs) from the output of gene families obtained from humann. To do so, I would like to use the most up-to-date version of the annotations linking the KO terms to the Uniref90 from uniprot database.

In other posts on this forum I have found that the humann utility map accesory files are built by parsing the uniprot DAT references: Index of /pub/databases/uniprot/knowledgebase

From here I have a couple of questions:

  1. To build the map_ko_uniref90.txt file you have parse the UniProtKB/Swiss-Prot reference (uniprot_sprot.dat.gz) or UniProtKB/TrEMBL (uniprot_trembl.dat.gz)?

  2. I can’t find the KO in this file, am I doing the process wrong or I need to perform any extra step?

Thank you very much in advance,
Irene

2

Historically the UniProt to KEGG Orthogroup mapping was contained on DR lines from these DAT files. However, checking a current example:

https://rest.uniprot.org/uniprotkb/Q99798.txt

This appears to no longer be the case. The only KEGG cross-reference is to the KEGG gene ID but not the KO term, which is challenging.