PeroxiBase: the peroxidase database.
Peroxidases (EC 1.11.1.x), which are encoded by small or large multigenic families, are involved in several important physiological and developmental processes. Analyzing their evolution and their distribution among various phyla could certainly help to elucidate the mystery of their extremely widespread and diversified presence in almost all living organisms. PeroxiBase was originally created for the exhaustive collection of class III peroxidase sequences from plants (Bakalovic, N., Passardi, F., et al., 2006. PeroxiBase: a class III plant peroxidase database. Phytochemistry 67, 534-539). The extension of the class III peroxidase database to all proteins capable to reduce peroxide molecules appears as a necessity. Our database contains haem and non-haem peroxidase sequences originated from annotated or not correctly annotated sequences deposited in the main repositories such as GenBank or UniProt KnowledgeBase. This new database will allow obtaining a global overview of the evolution the protein families and superfamilies capable of peroxidase reaction. In this rapidly growing field, there is a need for continual updates and corrections of the peroxidase protein sequences. Following the lack of unified nomenclature, we also introduced a unique abbreviation for each different family of peroxidases. This paper thus aims to report the evolution of the PeroxiBase database, which is freely accessible through a web server (http://peroxibase.isb-sib.ch). In addition to new categories of peroxidases, new specific tools have been created to facilitate query, classification and submission of peroxidase sequences.
Passardi
Filippo
F
Laboratory of Plant Physiology, University of Geneva, Quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland.
Theiler
Grégory
G
Zamocky
Marcel
M
Cosio
Claudia
C
Rouhier
Nicolas
N
Teixera
Felipe
F
Margis-Pinheiro
Marcia
M
Ioannidis
Vassilios
V
Penel
Claude
C
Falquet
Laurent
L
Dunand
Christophe
C
D030541:Databases, Genetic; D010544:Peroxidases / Q000737:chemistry* / Q000145:classification / Q000235:genetics; D010802:Phylogeny; D010944:Plants / Q000201:enzymology* / Q000235:genetics
D010544:Peroxidases