I downloaded virulence factor database from here , to predict virulence genes from few genomes that my lab sequenced. I performed local blast on the database with default setting and found around 4000 genes. I want to filter this result. I am not sure how to proceed. There are evalue, pident (percent identity), qcovs (query coverage) etc that I can tweak and I did tweak. For example, if I set pident above 40% the qcovs automatically goes close to 100%. That gave me indication above 40% is pretty significant and biologically relevant. But I am not sure what percent I should consider for treating the query as having the same function as the subject -- in this case that function is virulence.
Need some guidance.
Edit1: I ran blastp
Edit2: I am blasting protein (cds predicted from genome by annotation tool prokka). My question here is what is the most reasonable way to filter putative virulence factor using blast.