Table_4.xls (9.5 kB)

General characteristics of functional genes specifically present or absent in strains belonging to the main phylogenetic groups or exhibiting a specific phenotype.

dataset

posted on 2009-01-23, 00:36 authored by Marie Touchon, Claire Hoede, Olivier Tenaillon, Valérie Barbe, Simon Baeriswyl, Philippe Bidet, Edouard Bingen, Stéphane Bonacorsi, Christiane Bouchier, Odile Bouvet, Alexandra Calteau, Hélène Chiapello, Olivier Clermont, Stéphane Cruveiller, Antoine Danchin, Médéric Diard, Carole Dossat, Meriem El Karoui, Eric Frapy, Louis Garry, Jean Marc Ghigo, Anne Marie Gilles, James Johnson, Chantal Le Bouguénec, Mathilde Lescat, Sophie Mangenot, Vanessa Martinez-Jéhanne, Ivan Matic, Xavier Nassif, Sophie Oztas, Marie Agnès Petit, Christophe Pichon, Zoé Rouy, Claude Saint Ruf, Dominique Schneider, Jérôme Tourret, Benoit Vacherie, David Vallenet, Claudine Médigue, Eduardo P. C. Rocha, Erick Denamur

Functions were assigned according to E. coli K-12 MG1655 orthologous gene annotations [96] if any, or to similarity results obtained using the MicroScope analysis pipeline described in [95]. The categories ‘Enzymes’, ‘Regulators’, ‘Transporters and carriers’ (‘carriers’ includes specialized electron-carrying proteins and electron-carrying subunits of enzymes), ‘Factors’ (such as transcription and translation factors, and chaperones), and ‘Membrane components and structures’ are from GenProtEC [125] ‘Product type’ annotations (i.e., types of molecular functions) (Supplementary Table 6). The number of genes in each category does not take into account genes from phage and insertion sequence (IS) origin.

Considering the complete genome of the strain HS (phylogenetic group A). (http://msc.jcvi.org/e_coli_and_shigella/escherichia_coli_hs/index.shtml).

Considering the complete genome of enteropathogenic strain E2348/69 (phylogenetic group B2) (http://www.sanger.ac.uk/Projects/Escherichia_Shigella/). This strain is not virulent (0 of 10 mice killed) in the mouse model of extraintestinal virulence [32].

Genes on the virulence plasmid [56], not detailed in the subsequent columns.