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. In these cases, the rules will not work independently, but will be called by another rule, which will be triggered by a profile.

In addition to these rules corresponding to a unique PROSITE motif, there are also rules triggered by a specific combination of PROSITE motifs called metamotifs. Metamotifs allow the definition of arrangements of domains separated by spacers of variable size, as well as the anchoring to the N- and/or C-termini and the exclusion of a PROSITE motif.

ProRule uses the UniRule format that is common to all types of rules created to annotate UniProtKB/Swiss-Prot, including the HAMAP rules. Each rule contains information used to provide template based annotation associated with the domain or family detected by the PROSITE motif. ProRule is used to create UniProtKB/Swiss-Prot lines with basic and complex annotation derived from the presence of the domain and of biologically critical amino acids: domain name and boundaries, EC number, function, keywords, associated PROSITE patterns, PTMs, active sites, disulfide bonds, etc.). ProRule contains notably the position of structurally and/or functionally critical amino acid(s), as well as the condition(s) they must fulfil to play their biological role(s). Part of these supplementary data are used by ScanProsite that not only provides the protein sequence matched by a profile, but also information about the relevance of biologically meaningful residues, like active sites, binding sites, post-translational modification sites or disulfide bonds, to help function determination [References].