I am trying to identify a homologue of a mammalian protein in a genome of very distant but eukaryotic species. I’ve used number of on-line homology search tools but without success. It is known that proteins in this species exhibit low level of homology to other eukaryotes in terms of primary amino acid sequence. There are strong biochemical evidences that proteins in question must share certain sequence homology in addition to high functional homology. I guess that there is a workflow (or algorithm) which was developed for identification of distant homologues rather than special software.
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