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The active site of serine proteases is shaped as a cleft where the polypeptide
substrate binds. Schechter
and Berger  labeled amino acid residues from N to C term of the
polypeptide substrate (Pi, ..., P3, P2, P1, P1', P2', P3', ..., Pj) and
their respective binding sub-sites
(Si,..., S3, S2, S1, S1', S2', S3',..., Sj) . The cleavage is catalyzed
between P1 and P1'.
Rawlings and Barrett [2,3] have proposed a classification of proteases in families and clans.
Families group sequences according to the alignment score of their catalytic domains. A sequence belong to a family if significance score of BLAST  is less than 0.0001 or greater than 6.0 for RDF  and ProfilSearch , with at least one of the catalytic domains of the sequence family. Serine proteases are coded from S1 to S35. Sub-families classify deeply divergent groups from the same family, as indicated by letters such as S2A, S2B, etc...
Clans, coded from SA to SF, group families with the same order of catalytic residues along the sequence and show the same 3D-fold of the catalytic domain. Proteases of the same clan should have a common ancestor. Global classifications of proteases are accessible in the Merops  and ExPASy  websites. An overview of the classification of serine proteases is displayed in the sequence index page of this site.
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