I want to do metabolic mapping of annotated bacterial genomes. I annotated my genomes with prokka (which delivers annotation and in such cases gene name and EC number) and I would like to know if there are modules/packages for Python/R that can do this kind of mapping.

So what I would like to know is what pathways are covered by available genes and to what extend. It is also of interest for me which genes cannot be mapped.

Any ideas?

Thank you.