In Article <313E139B.176F at pc029.pharm.nwu.edu>, John Hogenesch
<john at pc029.pharm.nwu.edu> wrote:
>Molecular evolutionary biologists,
> I'm writing a paper where we identify five new members
>of a gene family. This brings the total number of identified
>proteins in vertebrates to eight. In addition there are five
>Drosophila members of this family and one bacterial. What
>characteristics would make these proteins a superfamily, family,
>or subfamily? They all contain a conserved domain, and all but
>two contain a second domain shared by bunches of proteins. The
>splicing patterns of a couple of these proteins have been
>determined, and they are also conserved (in the conserved
>domains).
> Any insight would be appreciated, as I can't seem to
>find a cogent definition of these terms. I get the feeling
>people throw them around a lot.
Yep.
The earliest definition of a family that I have seen came from Dayhoff, who
proposed (decreed) that 50% identity was a family and anything related but
less so was a superfamily. That was about 25 years ago, and was based on a
much smaller set of protein sequences than are available now.
I suspect taht this discussion will get into the same kind of Jesuitical
hair-splitting that other taxonomic discussions often approach when the
issue of the criteria for higher order taxa comes up.
My preference when I am talking/writing is to define those terms narrowly
with respect to the specific sequences that I am talking about. That may
lack to global generality that one might wish for in a an ideal world, but
at least it tells your reader/listener what the terms mean for the material
being discussed.
Warren Gallin,
Department of Biological Sciences, University of Alberta
wgallin at gpu.srv.ualberta.ca
