Help! Definiition of superfamily, family, subfamily

[Bob Obar]

There are three further points that I think are relevant to this 
discussion (which used to seem like a settled issue). 
(1) Since so many interesting proteins are chimeras, we should 
really refer ONLY to the domains (or predicted domains) as being 
members of families, superfamilies, etc., rather than the proteins 
that comprise them; "family" membership does connote common descent,
and in many cases only a portion of a multi-domain protein can 
properly be referred to in this sense. 
(2) Since the primary distinction between a protein family and a 
superfamily is the degree to which a functional activity (or set of 
activities) is conserved, it is inappropriate to draw a firm 
conclusion based on sequence comparisons IN THE ABSENCE OF PROTEIN 
FUNCTIONAL INFORMATION.  This is not necessarily as important a 
distinction for GENE families/superfamilies though, since their 
functions can be more completely inferred from their sequences. 
(3) It's never been clear to me just how we should relate the 
concepts of protein family/superfamily, etc., to those of gene 
family/superfamily, etc.  And what about pseudogenes, synthetic 
genes, and knockouts?  And how should we NAME families?  The current
practice is to use the name of the first family member discovered, 
usually a poor choice.

Bob Obar
102063,2640 at compuserve.com
102063,2640 at compuserve.com