We have a dataset consisting of 580-some proteins and are trying to condense it down by functional group. As such we want to go from the existing Protein ID (e.g. P02647) to an EC number. I can't seem to find a reliable way of doing this, let alone doing it batch-wise. Any suggestions would be appreciated!
Indeed, not all proteins are enzymes.
To find all reviewed UniProtKB (Swiss-Prot) entries that are enzymes, and to get their corresponding EC number(s), you can use this query
Then click on "Columns" to customize your result view: remove all irrelevant columns, and add one for EC (start typing "EC ..." and use the autocompleted suggestion "EC number"), cf http://www.uniprot.org/help/customize.
Once you are happy with your result view, you can download it in tab-delimited format, e.g. (first 10 entries): http://www.uniprot.org/uniprot/?query=ec:*%20reviewed:yes&limit=10&format=tab&columns=id,ec