Help! Definiition of superfamily, family, subfamily

Arlin Stoltzfus arlin at is.dal.ca
Mon Mar 11 07:11:41 EST 1996


John Hogenesch <john at pc029.pharm.nwu.edu> wrote:
> . . . What 
>characteristics would make these proteins a superfamily, family, 
>or subfamily? 

As others have pointed out, there are no hard-and-fast rules.
The rules used in SCOP (Structural Classification of
Proteins) can be found on the SCOP introductory page:

http://scop.mrc-lmb.cam.ac.uk/scop/intro.html

Proteins are hard to classify for two reasons.  Lower taxonomic 
levels can be judged easily by sequence comparisons, so people
tend to do this.  However, this approach doesn't follow through
to the higher rankings, where one must switch to structural
criteria.  The highest level of organization in SCOP ("fold"
groups: mostly beta, mostly alpha, alpha+beta, and mixed)
is defined in terms of structural criteria that aren't even
intended to define groups related by descent from a common
ancestor.  

A second problem is that most biological classifications 
are inherently hierarchical and assume a hierarchical structure 
of the data.  This is violated by chimaeric proteins, which
represent a mixture of domains from different sources.  

Arlin Stoltzfus (arlin at is.dal.ca)
Department of Biochemistry
Dalhousie University
Halifax, NS  B3H 4H7 CANADA
ph. 902-494-3569; fax 902-494-3569





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