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. 2006 Jan 1;34(Database issue):D227-30.
doi: 10.1093/nar/gkj063.

The PROSITE database

Nicolas Hulo  1 , Amos Bairoch, Virginie Bulliard, Lorenzo Cerutti, Edouard De Castro, Petra S Langendijk-Genevaux, Marco Pagni, Christian J A Sigrist
Affiliations

The PROSITE database

Nicolas Hulo et al. Nucleic Acids Res. .

Abstract

The PROSITE database consists of a large collection of biologically meaningful signatures that are described as patterns or profiles. Each signature is linked to a documentation that provides useful biological information on the protein family, domain or functional site identified by the signature. The PROSITE database is now complemented by a series of rules that can give more precise information about specific residues. During the last 2 years, the documentation and the ScanProsite web pages were redesigned to add more functionalities. The latest version of PROSITE (release 19.11 of September 27, 2005) contains 1329 patterns and 552 profile entries. Over the past 2 years more than 200 domains have been added, and now 52% of UniProtKB/Swiss-Prot entries (release 48.1 of September 27, 2005) have a cross-reference to a PROSITE entry. The database is accessible at http://www.expasy.org/prosite/.

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Figures

Figure 1
Figure 1
Output of the ScanProsite web page. (a) The left protein is a classical ephrin receptor protein (ephrin B4 receptor protein) which is known to transduce a signal through its kinase domain (5). The right protein is also an ephrin receptor protein (human ephrin B6 receptor protein) but with an inactive kinase domain (6). The ProRule associated with the kinase domain identifies an active site in ephrin B4 receptor but not in ephrin B6 receptor (absent feature: active site). The canonical Asp residue at the active site position is replaced by a serine. (b) We used ScanProsite to identify orthologues of the ephrin B6 receptor in mammals, searching for proteins that have the same domain arrangement and have a putative inactive kinase domain. (c) We also identified with ScanProsite an uncharacterized plant subfamily of kinase receptors with a putative inactive kinase domain. The canonical aspartate residue at the active site position is replaced by a histidine. This kinase subfamily is conserved in various plant genomes. Both multiple sequence alignments were generated on the ScanProsite web page using the alignment with the kinase profile (PS50011).
See this image and copyright information in PMC

References

    1. Sigrist C.J.A., Cerutti L., Hulo N., Gattiker A., Falquet L., Pagni M., Bairoch A., Bucher P. PROSITE: a documented database using patterns and profiles as motif descriptors. Brief. Bioinform. 2002;3:265–274. - PubMed
    1. Hulo N., Sigrist C.J.A., Le Saux V., Langendijk-Genevaux P.S., Bordoli L., Gattiker A., De Castro E., Bucher P., Bairoch A. Recent improvements to the PROSITE database. Nucleic Acids Res. 2004;32:134–137. - PMC - PubMed
    1. Sigrist C.J.A., De Castro E., Langendijk-Genevaux P.S., Le Saux V., Bairoch A., Hulo N. ProRule: a new database containing functional and structural information on PROSITE profiles. Bioinformatics. 2005;21:4060–4066. - PubMed
    1. Gattiker A., Michoud K., Rivoire C., Auchincloss A.H., Coudert E., Lima T., Kersey P., Pagni M., Sigrist C.J.A., Lachaize C., et al. Automated annotation of microbial proteomes in SWISS-PROT. Comput. Biol. Chem. 2003;27:49–58. - PubMed
    1. Kullander K., Klein R. Mechanisms and functions of Eph and ephrin signalling. Nature Rev. Mol. Cell. Biol. 2002;7:475–486. - PubMed

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