David Vallenet

..An increasing number of projects are related to the study of environmental bacterial (meta)genomes that are able to metabolize a large variety of chemical compounds that may be of high industrial interest...

..In addition, MaGe allows for annotation curation and exploration of already published genomes from various genera (e.g. Yersinia, Bacillus and Neisseria). MaGe can be accessed at http://www.genoscope.cns.fr/agc/mage...

..Taken together, all these observations suggest that the genome contents of the 3 Acinetobacters compared are partly shaped by life in distinct ecological niches: human (and more largely hospital environment), louse, soil...

..This holds true for Neisseria meningitidis, one of the most feared human bacterial pathogens that causes meningitis and septicemia...

..The MICheck website is accessible at the following address: http://www.genoscope.cns.fr/agc/tools/micheck...

..To access new enzymatic reactions and new or alternative pathways, we investigated bacterial metabolism through analyses of uncultivated bacterial consortia...

..They provide a way to integrate various types of biological information in a single framework, providing a structured representation of available knowledge on the metabolism of the respective species...

..They encode L-ornithine racemase, (2R,4S)-2,4-diaminopentanoate dehydrogenase, and the two subunits of 2-amino-4-ketopentanoate thiolase. While described only for the Clostridiaceae to date, this pathway is shown to be more widespread...

..subtilis is an epiphyte). This should permit investigators to make reliable inferences to prepare validation experiments in a variety of domains of bacterial growth and development as well as build up accurate phylogenies...

..This finding supports the view that the cycle itself is centrally geared to the catabolic capabilities of this exceptionally versatile organism...

..The AMIGene web site is accessible at the following address: http://www.genoscope.cns.fr/agc/tools/amigene/index.html (Contact: sbocs@genoscope.cns.fr)...

..ebi.ac.uk/chebi/). The newly annotated sequence is deposited at the International Nucleotide Sequence Data Collaboration with accession number AL009126.4...

..Using a supervised method, we were yet able to identify small sets of reactions related to pathogenicity or commensalism. The quality of our reconstructed networks also makes them reliable bases for building metabolic models...

..Replication is a highly unsymmetrical process, and the presence of two polymerases is therefore not unexpected. Using comparative genomics, we explored whether other processes have evolved in parallel with each polymerase...

..A computational validation of the approach is discussed. Finally, we present a case study on the anaerobic allantoin degradation pathway in Escherichia coli K-12...

..Adding to its originality, P. haloplanktis further differs from its marine counterparts with recruitment of a plasmid origin of replication for its second chromosome...

..We identified twelve bacteria that possess these genes and thus are expected to ferment lysine, and their gene organization is discussed...

..The genome consists of two linear replicons. The genes involved in fluorine metabolism and in the biosynthesis of the antibiotic thienamycin were mapped on both replicons...

..This collection provides a new resource for the study of gene function by forward and reverse genetic approaches and constitutes a robust experimental data source for systems biology approaches...