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, on the basis of similarities in their sequences, into a limited number of families.

The ProRule section of PROSITE is constituted of manually created rules that can automatically generate annotation in the UniProtKB/Swiss-Prot format based on PROSITE motifs. In most cases rules are based on PROSITE profiles as they are more specific than patterns, but occasionally rules make use of patterns.

The standard IUPAC one letter code for the amino acids is used in PROSITE. The symbol 'x' is used for a position where any amino acid is accepted. Ambiguities are indicated by listing the acceptable amino acids for a given position, between square brackets '[ ]'. For example: [ALT] stands for Ala or Leu or Thr.

While other protein domain databases such as Pfam (5) aim to be comprehensive and to a maximum sequence coverage, PROSITE concentrates on precise functional characterization, which can be used for protein database annotation.