Hi Mohammad,

Firstly, I assume you have the crystal structure of your protein. Otherwise, all you can do is a sequence alignment. There are some fancy sequence alignments that takes structural information into account, but I would take them with a grain of salt (they rarely do any better than a simple BLAST search). Assuming you have the crystal structure, DaliLite is a good structural comparison server. It goes through the PDB and find anything with similar tertiary structure, but I am not sure if you can filter by organism, so you will have to go through them one by one.

Best regards,

Arthur

http://ekhidna.biocenter.helsinki.fi/dali_server/