I have to answer a question about a sub-task of my thesis: Can the bacteria X produce the protein Y?
I searched of course Google and BLAST. There is no data supporting that this specific bacteria ever produced this protein sequence.
However, my thesis supervisor wants me to go deeper, but I don't know how to do it in silico in a way to offer a proper answer.
What I'm thinking of doing with the data at hand is to create a DB on localhost with all the versions of the protein listed in BLAST (I'm using ruby, not sure how can I fetch all this data in FASTA format yet, but I'll figure it out), and all the strains of the bacteria listed in BLAST and perform a fuzzy string matching.
That's like brute-forcing. After I have a possible score I can get the closest score of them all, study it a bit and then submit my answer.
Is there any other way to attack this problem in order to submit a proper, at least partially polished answer?
NOTE: I don't have access to any lab, any experiment must be performed in silico.
 My supervisor believes that IF this bacteria needed this protein it WOULD be able to to produce it at will without undergoing mutations. And since his level of dedication and knowledge revolving molecular biology is scary, it's kind of hard to believe that he is wrong.