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. [1]

Proteins typically share greater sequence and function similarities with other subfamily members than they do with members of their wider family. [1] [2] For example, in the Structural Classification of Proteins database classification system, members of a subfamily share the same interaction interfaces and interaction partners. [3] 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, [4] motifs linked to function, [5] or phylogenetic clade. [6] [7] 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. 1 2 "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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