proteome download if not included in the reference set provided by uniprot

Question

[alexshauser]

I am looking for proteomes that are not included in the reference set provided by uniprot (they don't pop up on the uniprot/proteome search and are also not available from ENSEMBLE). However, it seems still to be possible to blastp against proteomes in which I am interested in ( e.g. tarsius syrichta, alligator mississippiensis ...). Is it somehow possible to download these proteomes from uniprot or somehwere else?

Answer 1

[lisa.johnson.cohen]

You can download a fasta of all protein sequence records from a species of interest in the UNIPROT database by searching the taxonomy section, like this: http://www.uniprot.org/taxonomy/?query=tarsius+syrichta&sort=score

[alexshauser]

But what I actually want is the whole predicted proteome not the few annotated proteins!