PIR CLASSIFICATION TERMINOLOGY  
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Superfamilies

Protein families will be clustered into "homeomorphic superfamilies". Sequences are homeomorphic if they can be aligned from end-to-end. In practice, we allow the amino and carboxyl ends to be ragged and moderate internal length variations (represented as gaps in the sequences). However, all members of the superfamily should have the same overall architecture, i.e., the same domains in the same order (except for domains missing due to alternative splicing or very recent genetic events). It is assumed, although in most cases this has not been investigated in detail, that the molecules in a homeomorphic superfamily share a common evolutionary history since the acquisition of their constituent domains. Thus, it should be valid to construct an evolutionary tree from the members of a homeomorphic superfamily. If two groups of proteins with the same architecture are shown to have come to that structure independently, they are appropriately separated into two homeomorphic superfamilies.

Homology Domains

Many types of domains have been found in diverse proteins. In common use, the term "immunoglobulin superfamily" refers to the collection of all proteins that contain an immunoglobulin-like domain. We call such a group a "homology domain superfamily". Any given protein sequence will be assigned to only one homeomorphic superfamily, but it may contain sequence segments belonging to several homology domain superfamilies.

More extensive discussions of the family, superfamily, and domain organization within the PIR-International database can be found elsewhere [Superfamily and domain, W.C. Barker, F. Pfeiffer, and D.G. George in: Methods in Protein Structure Analsyis, M.Z. Atassi and E. Appella, eds., Plenum Publishing, New York, pp. 473-481, 1995.][Superfamily classification in the PIR-International Protein Sequence Database,W.C. Barker, F. Pfeiffer, and D.G. George, Methods in Enzymol. 266: 59-71,1996.].


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Revised 12/8/98