After the reformatting (or during, if working with the uniref databases) it should be possible to extract only proteins matching a certain taxon, say only Bacteria. This could be done on the command line with --taxlimit superkingdom:Bacteria for instance or --taxlimit superkingdom Bacteria Archaea
After the reformatting (or during, if working with the uniref databases) it should be possible to extract only proteins matching a certain taxon, say only Bacteria. This could be done on the command line with
--taxlimit superkingdom:Bacteria
for instance or--taxlimit superkingdom Bacteria Archaea