How compare proteomes of two species?

Question

[saber mohammadi]

Hello everyone. I have two fasta files from two different species(Xylella fastidiosa and Aquifex aeolicus) which include protein sequences. I want to know whether there are any similarities between these two species? In other words, I want to compare their proteome. I don't know how to do this. Should I use blast? if yes, which kind of blast? or there are other more useful methods than blast!? I appreciate it if you could help me with this.

[Mark]

You could do multiple sequence alignment of the whole proteome/fasta files to match them. But what exact question are you trying to answer apart from protein X is similar to protein Y?

Are you interested in a specific gene or protein/enzyme/pathway you want to compare?

[GenoMax]

See a couple of past threads about this topic:
How To Compare Two Proteome Sets At 30% Similarity?
which tool to compare two proteomes ?

Without a more focused objective trying to compare proteins from two species which are from two different families can become a goose chase.

Lineage (full): cellular organisms; Bacteria; Aquificae; Aquificae; Aquificales; Aquificaceae; Aquifex<br>
Lineage (full): cellular organisms; Bacteria; Proteobacteria; Gammaproteobacteria; Xanthomonadales; Xanthomonadaceae; Xylella