Off topic:Phylogenetic Profiling on protein base

Question

[aamiralimbd]

Hello I am working on my M Phil thesis. It is on bioinformatics and my major is computer science. I am finding some difficulty regarding knowledge related to microbiology. So i need little help. I am working on phylogenetic profiles on base of proteins of S Pombe. I want to know, how i can check the presence of a protein in other organisms/genomes.

Actually I want to know what could be the common base to search a protein in different organisms. Locus Id is the position of gene on genome so how it could be used. Same protein can exist on there positions on different genome.

Thanks in advance for your time and help.