Help! Definiition of superfamily, family, subfamily

Warren Gallin wgallin at gpu.srv.ualberta.ca
Thu Mar 7 13:25:34 EST 1996


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



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