PROSITE is a database of protein families and domains. It is based on the observation that, while there is a huge number of different proteins, most of them can be grouped, by similarities in their sequences, into a limited number of families. Proteins or protein domains belonging to a particular family generally share functional attributes and are derived from a common ancestor.

It is apparent when studying protein sequence families that some regions have been better conserved than others during evolution. These regions are generally important for the function of a protein and/or for the maintenance of its three- dimensional structure. By analysing the constant and variable properties of such groups of similar sequences, it is possible to derive a signature for a protein family or domain, which distinguishes its members from all other unrelated proteins. A pertinent analogy is the use of fingerprints by the police for identification purposes. A fingerprint is generally sufficient to identify a given individual. Similarly, a protein signature can be used to assign a newly sequenced protein to a specific family of proteins and thus to formulate hypotheses about its function.

PROSITE currently contains signatures specific for about a thousand protein families or domains. Each of these signatures comes with documentation providing background information on the structure and function of these proteins.