I have identified a conserved region in a protein I'm studying, by doing multiple sequence alignments against a dozen of its orthologs. I've then found that this region also aligns relatively well with a functional region (binding motif) in a completely unrelated protein, and I'm trying to estimate whether it's reasonable to believe the two regions might be bound by the same protein. blastp doesn't identify this match, would I then assume that this is insignificant?
Let's say I have a 15 aa long peptide sequence X, which I align against a longer 200 aa protein sequence Y. I find some best match (gaps allowed).
What statistical test could I now perform to answer the question:
Is the match I found for sequence X in sequence Y significantly better than what I would expect to find between X and a random 200 aa sequence Z?