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. RefSeq:YP_805528.1.

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?

You can use Entrez Direct for this as follows:

efetch -db protein -id YP_805528.1 -format gpc -mode xml | xtract -insd Protein EC_number
YP_805528.1     6.3.2.13

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