title: An updated metabolic view of the Bacillus subtilis 168 genome.
abstract: Continuous updating of the genome sequence of Bacillus subtilis, the model of the Firmicutes, is a basic requirement needed by the biology community. In this work new genomic objects have been included (toxin/antitoxin genes and small RNA genes) and the metabolic network has been entirely updated. The curated view of the validated metabolic pathways present in the organism as of 2012 shows several significant differences from pathways present in the other bacterial reference, Escherichia coli: variants in synthesis of cofactors (thiamine, biotin, bacillithiol), amino acids (lysine, methionine), branched-chain fatty acids, tRNA modification and RNA degradation. In this new version, gene products that are enzymes or transporters are explicitly linked to the biochemical reactions of the RHEA reaction resource (http://www.ebi.ac.uk/rhea/), while novel compound entries have been created in the database Chemical Entities of Biological Interest (http://www.ebi.ac.uk/chebi/). The newly annotated sequence is deposited at the International Nucleotide Sequence Data Collaboration with accession number AL009126.4.
authors: UEVE, Université d'Evry, boulevard François Mitterrand, 91025 Evry, France.|CNRS-UMR 8030, 2 rue Gaston Crémieux, 91057 Evry, France.|CEA, Institut de Génomique, Génoscope Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme, 2 rue Gaston Crémieux, 91057 Evry, France.
authors: Eugeni
authors: E
authors: Belda
authors: AMAbiotics SAS, Bldg G1, 2 rue Gaston Crémieux, 91000 Evry, France.
authors: Agnieszka
authors: A
authors: Sekowska
authors: UEVE, Université d'Evry, boulevard François Mitterrand, 91025 Evry, France.|CNRS-UMR 8030, 2 rue Gaston Crémieux, 91057 Evry, France.|CEA, Institut de Génomique, Génoscope Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme, 2 rue Gaston Crémieux, 91057 Evry, France.
authors: François
authors: F
authors: Le Fèvre
authors: Swiss Institute of Bioinformatics, CMU, 1 Michel-Servet, CH-1211 Genève 4, Switzerland.
authors: Anne
authors: A
authors: Morgat
authors: UEVE, Université d'Evry, boulevard François Mitterrand, 91025 Evry, France.|CNRS-UMR 8030, 2 rue Gaston Crémieux, 91057 Evry, France.|CEA, Institut de Génomique, Génoscope Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme, 2 rue Gaston Crémieux, 91057 Evry, France.
authors: Damien
authors: D
authors: Mornico
authors: Department of Biochemistry, Li KaShing Faculty of Medicine, The University of Hong Kong, 21, Sassoon Road, Hong Kong SAR, China.|Institute of Applied Biosciences, Centre for Research and Technology Hellas (CERTH), Thessaloniki, Greece.
authors: Christos
authors: C
authors: Ouzounis
authors: UEVE, Université d'Evry, boulevard François Mitterrand, 91025 Evry, France.|CNRS-UMR 8030, 2 rue Gaston Crémieux, 91057 Evry, France.|CEA, Institut de Génomique, Génoscope Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme, 2 rue Gaston Crémieux, 91057 Evry, France.
authors: David
authors: D
authors: Vallenet
authors: UEVE, Université d'Evry, boulevard François Mitterrand, 91025 Evry, France.|CNRS-UMR 8030, 2 rue Gaston Crémieux, 91057 Evry, France.|CEA, Institut de Génomique, Génoscope Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme, 2 rue Gaston Crémieux, 91057 Evry, France.
authors: Claudine
authors: C
authors: Médigue
authors: Department of Biochemistry, Li KaShing Faculty of Medicine, The University of Hong Kong, 21, Sassoon Road, Hong Kong SAR, China.|AMAbiotics SAS, Bldg G1, 2 rue Gaston Crémieux, 91000 Evry, France.
authors: Antoine
authors: A
authors: Danchin
mesh_terms: D001412:Bacillus subtilis / Q000235:genetics / Q000378:metabolism*; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D016680:Genome, Bacterial; D023281:Genomics; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA
chemical_list: D001426:Bacterial Proteins