I annotated my bacterial genomes using the new NCBI Prokaryotic Genome Annotation Pipeline and now, I want to annotate EC-numbers.
In the master annotation file (.gff), I get the RefSeq-ID of every successful annotation, e.g.
When I visit the respective NCBI page, I see that it sometimes is mapped to an EC number.
I'd like to automate this process: Convert every RefSeq-ID to an EC number. How can I do this?
(I may already have discovered the first step: I can map the RefSeq-ID to the NCBI-ID (Entrez-ID) using this NCBI conversion database:
YP_805528.1 -> 4419225. But I don't see how to get from these databases to EC.)
Are there other ways? As far as I know, most people blast their genes to already-mapped databases like SwissProt and ExPASy ENZYME. But I don't like this approach because technically, the NCBI annotation pipeline already did this. Why compute the same thing twice?