Prosite, a constituent of the ExPASy proteomics analysis server, is a protein database that classifies protein families and domains, functional sites within proteins and also amino acid patterns. Prosite is modeled around consideration of the fact that although there is an immense amount of different proteins, most can be categorized and grouped into a limited number of families based on similarities within their sequences. By analyzing the consistent and varying properties of groups maintaining similar sequences that have been conserved over the course of evolution, this database allows for the potential derivation of a ‘signature’ for protein families or domains. Prosite provides specific profiles for


Fig. 1 Prosite Database Search Engine

over a thousand protein families, and each signature also comes with documentation that provides background information on the structure and function of the specific proteins. The use of these signatures allows for newly sequenced proteins to be assigned to a particular protein family and thus their functionality can be tested to validate or contradict hypotheses.  Other uses of Prosite include sequence analysis, motif detection, PRATT (a tool that allows interactive generation of conserved patterns from a series of unaligned proteins), and an image creator that allows generation of custom domain figures. 


All entries found in Prosite were manually curated by a team from the Swiss Institute of Bioinformatics and are integrated into Swiss-Plot protein annotation. Prosite was created in 1988 by Amos Bairoch, a director of the Swiss Institute of Bioninformatics for more than 20 years. As of July, 2009, however, the director of the Prosite database (along with Swiss-Prot and Vital-IT groups) is Loannis Xenarios. 

Accessing the DatabaseEdit

Using the Zinc Finger Motif as an example;

1. Type name of motif (Zinc Finger) into Prosite Access search bar. Other browsing categories include documentation entry, Prorule description, taxonomic scope and number of positive hits.

2. All documents in Prosite containing the desired search word will appear on the search results page. To delve deeper into a particular domain profile, simply click on a document on the list (we will click on ARF GTPase-activating proteins domain profile).

3. The description section should describe the domain and its biological importance in some detail. It also should describe the desired search word (Zinc Finger Motif) and its contribution to the domain importance in its entirety. A technical section is also present in which a large number of tools allow access to anything within the database relating to your specific search through Swiss-Prot/UniProtKB classification. 

4. Click on ‘Prosite Domain Architechture View…’ to display the Prosite matches on all Swiss-Prot entries with at least one match to the entry of interest (ARF GTPase-activating protein – PS50115) along with rule-based predicted features inside matches. To obtain details of the pred


icted features, the ScanProsite tool link should be on the right of each image.


Prosite. (2008, August 16). In Wikipedia, The Free Encyclopedia. Retrieved 14:50, September 15, 2013, from