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==Terminology and usage==
As with many biological terms, the use of ''protein family'' is somewhat context dependent; it may indicate large groups of proteins with the lowest possible level of detectable sequence similarity, or very narrow groups of proteins with almost identical sequence, function, and three-dimensional structure, or any kind of group in-between. To distinguish between these situations, the term [[protein superfamily]] is often used for distantly related proteins whose relatedness is not detectable by sequence similarity, but only from shared structural features.<ref name="pmid4435228">{{cite journal | vauthors = Dayhoff MO | title = Computer analysis of protein sequences | journal = Federation Proceedings | volume = 33 | issue = 12 | pages = 2314–6 | date = December 1974 | pmid = 4435228 }}</ref><ref>{{Cite journal | vauthors = Dayhoff MO, McLaughlin PJ, Barker WC, Hunt LT | author-link1 =Margaret Oakley Dayhoff | title = Evolution of sequences within protein superfamilies | doi = 10.1007/BF00608697 | journal = Die Naturwissenschaften | volume = 62 | issue = 4 | pages = 154–161 | year = 1975 | bibcode=1975NW.....62..154D| s2cid =40304076 }}</ref><ref name="pmid181273">{{cite journal | vauthors = Dayhoff MO | title = The origin and evolution of protein superfamilies | journal = Federation Proceedings | volume = 35 | issue = 10 | pages = 2132–8 | date = August 1976 | pmid = 181273 }}</ref> Other terms such as protein ''class'', ''group'', ''clan'' and ''sub-family'' have been coined over the years, but all suffer similar ambiguities of usage. A common usage is that superfamilies ([[structural homology]]) contain families ([[sequence homology]]) which contain [[protein subfamily|sub-families]]. Hence a superfamily, such as the [[PA clan]] of proteases, has far lower sequence conservation than one of the families it contains, the C04 family. It is unlikely that an exact definition will be agreed and to it is up to the reader to discern exactly how these terms are being used in a particular context.
{{wide image|PA clan vs C04 family sequence conservation.png|1000px|Above, [[sequence conservation]] of 250 members of the [[PA clan]] [[proteases]] ([[superfamily (molecular biology)|superfamily]]). Below, sequence conservation of 70 members of the C04 protease family. Arrows indicate [[catalytic triad]] residues. Aligned on the basis of [[structure]] by [[Families of structurally similar proteins|DALI]]}}
==Protein domains and motifs==
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