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Nucleic Acids Res. 2009 Jan;37(Database issue):D261-6. doi: 10.1093/nar/gkn680. Epub 2008 Oct 23.

PeroxiBase: a database with new tools for peroxidase family classification.

Author information

1
Swiss Institute of Bioinformatics, Swiss-Prot Group, CMU, 1 rue Michel Servet, Laboratory of Plant Physiology, University of Geneva, Quai Ernest-Ansermet 30, CH-1211 Geneva, Switzerland.

Abstract

Peroxidases (EC 1.11.1.x), which are encoded by small or large multigenic families, are involved in several important physiological and developmental processes. They use various peroxides as electron acceptors to catalyse a number of oxidative reactions and are present in almost all living organisms. We have created a peroxidase database (http://peroxibase.isb-sib.ch) that contains all identified peroxidase-encoding sequences (about 6000 sequences in 940 organisms). They are distributed between 11 superfamilies and about 60 subfamilies. All the sequences have been individually annotated and checked. PeroxiBase can be consulted using six major interlink sections 'Classes', 'Organisms', 'Cellular localisations', 'Inducers', 'Repressors' and 'Tissue types'. General documentation on peroxidases and PeroxiBase is accessible in the 'Documents' section containing 'Introduction', 'Class description', 'Publications' and 'Links'. In addition to the database, we have developed a tool to classify peroxidases based on the PROSITE profile methodology. To improve their specificity and to prevent overlaps between closely related subfamilies the profiles were built using a new strategy based on the silencing of residues. This new profile construction method and its discriminatory capacity have been tested and validated using the different peroxidase families and subfamilies present in the database. The peroxidase classification tool called PeroxiScan is accessible at the following address: http://peroxibase.isb-sib.ch/peroxiscan.php.

PMID:
18948296
PMCID:
PMC2686439
DOI:
10.1093/nar/gkn680
[Indexed for MEDLINE]
Free PMC Article

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