I am interested in a small domain of a well studied and well defined protein (Huntingtin), and would like to see how conserved this domain is across species. In particular, I would like to address two questions in a scientific (publishable) way:
How well conserved across species is this domain relative to the rest of the protein and relative to other proteins in general?
How far can I go from humans (evolutionary speaking) and find that this domain is still very similar (say >90% sequence identity) to what is found in humans?
Sorry if this is unclear, or has already been addressed. I tried to search for questions that addressed these issues but could not find anything. I have tried BLASTing the protein sequence, but that just gets me close relatives (e.g. chimps) that are almost identical. I am actually more interested in distant relatives. Any helpful program(s) or methods would be greatly appreciated.
Thanks a lot in advance for your help.