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Protein subfamily

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Protein subfamily is a level of protein classification, based on their close evolutionary relationship. It is below the larger levels of protein superfamily and protein family.

Proteins typically share greater sequence and function similarities with other subfamily members than they do with members of their wider family. For example, in the Structural Classification of Proteins database classification system, members of a subfamily share the same interaction interfaces and interaction partners. These are stricter criteria than for a family, where members have similar structures, but may be more distantly related and so have different interfaces. Subfamilies are assigned by a variety of methods, including sequence similarity, motifs linked to function, or phylogenetic clade. There is no exact and consistent distinction between a subfamily and a family. The same group of proteins may sometimes be described as a family or a subfamily, depending on the context.

References

  1. ^ "What are protein families?". EMBL-EBI Train online. 2011-11-18. Retrieved 2018-03-08.
  2. Das, Sayoni; Orengo, Christine A. (2016). "Protein function annotation using protein domain family resources" (PDF). Methods. 93: 24–34. doi:10.1016/j.ymeth.2015.09.029. PMID 26434392.
  3. Rausell, Antonio; Juan, David; Pazos, Florencio; Valencia, Alfonso (2010-02-02). "Protein interactions and ligand binding: From protein subfamilies to functional specificity". Proceedings of the National Academy of Sciences. 107 (5): 1995–2000. Bibcode:2010PNAS..107.1995R. doi:10.1073/pnas.0908044107. PMC 2808218. PMID 20133844.
  4. Brown, Duncan P.; Krishnamurthy, Nandini; Sjölander, Kimmen (2007-08-17). "Automated Protein Subfamily Identification and Classification". PLOS Computational Biology. 3 (8): e160. Bibcode:2007PLSCB...3..160B. doi:10.1371/journal.pcbi.0030160. ISSN 1553-7358. PMC 1950344. PMID 17708678.
  5. Eisen, Jonathan A.; Sweder, Kevin S.; Hanawalt, Philip C. (1995-07-25). "Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions". Nucleic Acids Research. 23 (14): 2715–2723. doi:10.1093/nar/23.14.2715. ISSN 0305-1048. PMC 307096. PMID 7651832.
  6. Wicker, Nicolas; Perrin, Guy René; Thierry, Jean Claude; Poch, Olivier (2001-08-01). "Secator: A Program for Inferring Protein Subfamilies from Phylogenetic Trees". Molecular Biology and Evolution. 18 (8): 1435–1441. doi:10.1093/oxfordjournals.molbev.a003929. ISSN 0737-4038. PMID 11470834.
  7. Mi, Huaiyu; Poudel, Sagar; Muruganujan, Anushya; Casagrande, John T.; Thomas, Paul D. (2016-01-04). "PANTHER version 10: expanded protein families and functions, and analysis tools". Nucleic Acids Research. 44 (D1): D336 – D342. doi:10.1093/nar/gkv1194. ISSN 0305-1048. PMC 4702852. PMID 26578592.

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