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 SCOP 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.

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Protein family group of proteins that share a common evolutionary origin, reflected by similarity in their sequence

A protein family is a group of evolutionarily-related proteins. In many cases a protein family has a corresponding gene family, in which each gene encodes a corresponding protein with a 1:1 relationship. The term protein family should not be confused with family as it is used in taxonomy.

Structural Classification of Proteins database

The Structural Classification of Proteins (SCOP) database is a largely manual classification of protein structural domains based on similarities of their structures and amino acid sequences. A motivation for this classification is to determine the evolutionary relationship between proteins. Proteins with the same shapes but having little sequence or functional similarity are placed in different superfamilies, and are assumed to have only a very distant common ancestor. Proteins having the same shape and some similarity of sequence and/or function are placed in "families", and are assumed to have a closer common ancestor.

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Rfam is a database containing information about non-coding RNA (ncRNA) families and other structured RNA elements. It is an annotated, open access database originally developed at the Wellcome Trust Sanger Institute in collaboration with Janelia Farm, and currently hosted at the European Bioinformatics Institute. Rfam is designed to be similar to the Pfam database for annotating protein families.

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A protein superfamily is the largest grouping (clade) of proteins for which common ancestry can be inferred. Usually this common ancestry is inferred from structural alignment and mechanistic similarity, even if no sequence similarity is evident. Sequence homology can then be deduced even if not apparent. Superfamilies typically contain several protein families which show sequence similarity within each family. The term protein clan is commonly used for protease and glycosyl hydrolases superfamilies based on the MEROPS and CAZy classification systems.

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References

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  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. 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. 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.
  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.