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SORGOdb: Superoxide Reductase Gene Ontology curated DataBase.

Lucchetti-Miganeh C, Goudenège D, Thybert D, Salbert G, Barloy-Hubler F - BMC Microbiol. (2011)

Bottom Line: Superoxide reductases (SOR) catalyse the reduction of superoxide anions to hydrogen peroxide and are involved in the oxidative stress defences of anaerobic and facultative anaerobic organisms.These genes, named sor, are short and the transfer of annotations from previously characterized neelaredoxin, desulfoferrodoxin, superoxide reductase and rubredoxin oxidase has been heterogeneous.SORGOdb contains 325 non-redundant and curated SOR, from 274 organisms.

View Article: PubMed Central - HTML - PubMed

Affiliation: CNRS UMR 6026, ICM, Equipe Sp@rte, Université de Rennes 1, Campus de Beaulieu, 35042 Rennes, France. celine.lucchetti@univ-rennes1.fr

ABSTRACT

Background: Superoxide reductases (SOR) catalyse the reduction of superoxide anions to hydrogen peroxide and are involved in the oxidative stress defences of anaerobic and facultative anaerobic organisms. Genes encoding SOR were discovered recently and suffer from annotation problems. These genes, named sor, are short and the transfer of annotations from previously characterized neelaredoxin, desulfoferrodoxin, superoxide reductase and rubredoxin oxidase has been heterogeneous. Consequently, many sor remain anonymous or mis-annotated.

Description: SORGOdb is an exhaustive database of SOR that proposes a new classification based on domain architecture. SORGOdb supplies a simple user-friendly web-based database for retrieving and exploring relevant information about the proposed SOR families. The database can be queried using an organism name, a locus tag or phylogenetic criteria, and also offers sequence similarity searches using BlastP. Genes encoding SOR have been re-annotated in all available genome sequences (prokaryotic and eukaryotic (complete and in draft) genomes, updated in May 2010).

Conclusions: SORGOdb contains 325 non-redundant and curated SOR, from 274 organisms. It proposes a new classification of SOR into seven different classes and allows biologists to explore and analyze sor in order to establish correlations between the class of SOR and organism phenotypes. SORGOdb is freely available at http://sorgo.genouest.org/index.php.

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Related in: MedlinePlus

A snapshot of the SORGOdb input interface. (A) The "Browse By Phylogeny" module allows the selection of organisms with an SOR, using complete phylogeny criteria (kingdom, phylum, class and order). (B) The results panel provides intermediary selection options and displays SOR record information in a tabular way including organism name, locus tag name, SORGOdb classification and domain architecture. (C) Using checkboxes, amino acid sequences and bibliography links can be obtained and the synopsis can be downloading in .pdf format.
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Figure 1: A snapshot of the SORGOdb input interface. (A) The "Browse By Phylogeny" module allows the selection of organisms with an SOR, using complete phylogeny criteria (kingdom, phylum, class and order). (B) The results panel provides intermediary selection options and displays SOR record information in a tabular way including organism name, locus tag name, SORGOdb classification and domain architecture. (C) Using checkboxes, amino acid sequences and bibliography links can be obtained and the synopsis can be downloading in .pdf format.

Mentions: SORGOdb includes both documentation and search options. The web interface is composed of two panels (Figure 1).


SORGOdb: Superoxide Reductase Gene Ontology curated DataBase.

Lucchetti-Miganeh C, Goudenège D, Thybert D, Salbert G, Barloy-Hubler F - BMC Microbiol. (2011)

A snapshot of the SORGOdb input interface. (A) The "Browse By Phylogeny" module allows the selection of organisms with an SOR, using complete phylogeny criteria (kingdom, phylum, class and order). (B) The results panel provides intermediary selection options and displays SOR record information in a tabular way including organism name, locus tag name, SORGOdb classification and domain architecture. (C) Using checkboxes, amino acid sequences and bibliography links can be obtained and the synopsis can be downloading in .pdf format.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3116461&req=5

Figure 1: A snapshot of the SORGOdb input interface. (A) The "Browse By Phylogeny" module allows the selection of organisms with an SOR, using complete phylogeny criteria (kingdom, phylum, class and order). (B) The results panel provides intermediary selection options and displays SOR record information in a tabular way including organism name, locus tag name, SORGOdb classification and domain architecture. (C) Using checkboxes, amino acid sequences and bibliography links can be obtained and the synopsis can be downloading in .pdf format.
Mentions: SORGOdb includes both documentation and search options. The web interface is composed of two panels (Figure 1).

Bottom Line: Superoxide reductases (SOR) catalyse the reduction of superoxide anions to hydrogen peroxide and are involved in the oxidative stress defences of anaerobic and facultative anaerobic organisms.These genes, named sor, are short and the transfer of annotations from previously characterized neelaredoxin, desulfoferrodoxin, superoxide reductase and rubredoxin oxidase has been heterogeneous.SORGOdb contains 325 non-redundant and curated SOR, from 274 organisms.

View Article: PubMed Central - HTML - PubMed

Affiliation: CNRS UMR 6026, ICM, Equipe Sp@rte, Université de Rennes 1, Campus de Beaulieu, 35042 Rennes, France. celine.lucchetti@univ-rennes1.fr

ABSTRACT

Background: Superoxide reductases (SOR) catalyse the reduction of superoxide anions to hydrogen peroxide and are involved in the oxidative stress defences of anaerobic and facultative anaerobic organisms. Genes encoding SOR were discovered recently and suffer from annotation problems. These genes, named sor, are short and the transfer of annotations from previously characterized neelaredoxin, desulfoferrodoxin, superoxide reductase and rubredoxin oxidase has been heterogeneous. Consequently, many sor remain anonymous or mis-annotated.

Description: SORGOdb is an exhaustive database of SOR that proposes a new classification based on domain architecture. SORGOdb supplies a simple user-friendly web-based database for retrieving and exploring relevant information about the proposed SOR families. The database can be queried using an organism name, a locus tag or phylogenetic criteria, and also offers sequence similarity searches using BlastP. Genes encoding SOR have been re-annotated in all available genome sequences (prokaryotic and eukaryotic (complete and in draft) genomes, updated in May 2010).

Conclusions: SORGOdb contains 325 non-redundant and curated SOR, from 274 organisms. It proposes a new classification of SOR into seven different classes and allows biologists to explore and analyze sor in order to establish correlations between the class of SOR and organism phenotypes. SORGOdb is freely available at http://sorgo.genouest.org/index.php.

Show MeSH
Related in: MedlinePlus