Mapping NCBI nr protein database to KEGG orthology

Question

[RandyLahey]

I would like to map sequences aligned to the NCBI's nr protein database to KO identifiers for functional analysis. I can get Uniprot identifiers mapped to KO identifiers by downloading the uniprot to KO link via the rest API, but can't seem to do the same for the NCBI's nr protein database. Does anyone know if this is possible? Thanks.

Answer 1

[Mark]

You're after the RefSeq database. Use uniprot to find the refseq IDs of the proteins of interest. I actually think you'd get all the info you need from uniprot alone. Here's an example. Unless uniprot doesn't contain the organism/genes of interest. But I find they usually do.

When searching for an organism/gene if you click on the pen or column button it will allow you to add or modify the data. KEGG ids can be found under Sequences and the KO numbers can be found under Phylogenomics.