Close homologs search


I have a group of bacterial proteins that are very close to each other (this means that they are in a big group, but form a subgroup with distinctive features) and share some biochemical properties and I have to find homologous proteins from thermophiles that belong to this group and have the same properties as well. Is it good to just "BLAST" every protein against the database, find proteins from thermophiles, and build a tree to find proteins that belong to this subgroup? I've also tried to make PSSM from proteins that I have and to search with PSI-BLAST using this PSSM instead of the classic matrix.





You have a contradiction between your title and the subsequent explanation, so it is not clear what you want. If you want "close homologs" only, plain BLASTP will most likely be sufficient. PSSMs are explicitly meant for diversifying the profile and iterating the search to find distant homologs. Unless your aim is to find ALL homologs - doesn't seem to be that way - I think you will do just fine with BLASTP because it most definitely will be able to find close homologs, and even many that are not so close.

Separately, I am curious how will you decide what are thermophiles in your search results? Are you really able to look at species name and know whether it is a thermophile?

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