I'm trying to map the presence of three different proteins over the bacterial kingdom. First I thought of using pfam for this purpose, but two proteins end up in very messy DUFs (Domein of Unknown Function). So I now ran three BLAST queries on the Representative Proteomes (http://pir.georgetown.edu/rps/) and put an e-value threshold of 10-5 in place.
This results for each protein in a BLAST table that contains both an UniProt Proteome Identifier and a NCBI Taxonomy identifiers.
Now I want to map back these BLAST results to either a Uniprot taxonomy or NCBI taxonomy. For the NCBI taxonomy there is a tool available http://www.ncbi.nlm.nih.gov/Taxonomy/CommonTree/wwwcmt.cgi however does a similar taxonomy tool exist for the Uniprot as well? Preferably I would supply it with a list of Uniprot Proteome identifiers and it would return a tree (in for example) phylip format. This could then be visualized using iTOL. I found a neat translation between Uniprot and the NCBI taxonomy (http://www.uniprot.org/docs/speclist.txt) but I was wondering if a Uniprot taxonomy exist as well?