KEGG annotations - the number is much lower number than expected

[tvtv195]

Dear bakta team,
We ran bakta on several bacterial genomes, with >50% estimated compl. and <10% contam., to obtain KEGG annotations.
Bakta ran just fine, without any issues, e.g.:

bakta --db /gpfs/gpfs1/scratch/cb761220/databases/bakta_db_2024/db
-o /scratch/cb761203/02.analysis/13.module13/01.bakta/ -v
/scratch/cb761203/02.analysis/12.module12/bins_hq/sample.bin.35.fa

However, we only got between 0 and 17 KEGG annotations (K0 ID) per genome.
For example, a very small bacterial genome of 531,276 bp had 517 CDS but not even a single KEGG annotation.

Is there something wrong with the way bakta assigns KEGG annotations?
Best,
Chris

[oschwengers]

Hi Chris, and thanks for reaching out. Based on the command line above, I guess you're working on a MAG. Depending on the species it could simply be the case that there are only few to no genes similar to those stored in KEGG. Could you provide some information about how many UniRef90-annotated genes and how many hypotheticals you get ?