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Peptidases, families, and clans

Part 3. Proteomics

3.6. Proteome Families

Specialist Review

  1. Neil D. Rawlings,
  2. Alan J. Barrett

Published Online: 15 APR 2005

DOI: 10.1002/047001153X.g306216

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Rawlings, N. D. and Barrett, A. J. 2005. Peptidases, families, and clans. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 3:3.6:80.

Author Information

  1. Wellcome Trust Sanger Institute, Cambridge, UK

Publication History

  1. Published Online: 15 APR 2005


Peptidases (all proteolytic enzymes) are classified in a hierarchical system on the basis of evolutionary relationships. An identifier is assigned to each distinctive peptidase, and for each amino acid sequence, properties including the limits of the peptidase unit and the positions of the active site residues are recorded. The peptidase unit is the part of the molecule directly responsible for peptidase activity, and sequence comparisons are made only with this to exclude false-positive matches with nonpeptidase domains. The peptidases are grouped in families, each of which contains a type-example peptidase and all the peptidases that can be shown to be related to it either directly or indirectly (transitively). Families that show evidence of being homologous are grouped together in a clan, so each clan is intended to contain the modern-day representatives of a single origin of peptidases. The evidence for homology of families comes from similarities in protein fold as well as the arrangement of active site residues and motifs in the sequence. A clan may contain just a single family with a unique structure. The classification forms the logical structure of the MEROPS database (, which also includes a summary, structural representation, and bibliography for each peptidase, family, and clan, a sequence alignment for each family and clan, and a tree for each family.


  • peptidase;
  • protease;
  • proteinase;
  • classification;
  • MEROPS database;
  • proteolytic enzyme