I am studying 3 proteins from the same family and I have performed an CLUSTALw alignment of each protein. It comes from their origin (fishes or amphibians depends) to primates. Afterthat with the human protein and PROSITE database I have scanned for patterns and profiles to check if these patterns are conserved in the CLUSTALw alignment. Now, without considering the regions that showed a pattern, I still have regions very conserved.
So then, I would like to know if there is a way to know the role of these regions. I have been looking for in literature or in a database of regular expression.... but does anyone an idea?
The regions comes from 2-3 aa to a maximun of 15-16 aa. They are transmembrane proteins. The conserved regions are out of the TM domain.