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

a<p>Functions were assigned according to <i>E. coli</i> K-12 MG1655 orthologous gene annotations <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000344#pgen.1000344-Riley1" target="_blank">[96]</a> if any, or to similarity results obtained using the MicroScope analysis pipeline described in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000344#pgen.1000344-Vallenet2" target="_blank">[95]</a>. 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 <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000344#pgen.1000344-Serres1" target="_blank">[125]</a> ‘Product type’ annotations (i.e., types of molecular functions) (Supplementary <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000344#pgen-1000344-t006" target="_blank">Table 6</a>). The number of genes in each category does not take into account genes from phage and insertion sequence (IS) origin.</p>b<p>Considering the complete genome of the strain HS (phylogenetic group A). (<a href="http://msc.jcvi.org/e_coli_and_shigella/escherichia_coli_hs/index.shtml" target="_blank">http://msc.jcvi.org/e_coli_and_shigella/escherichia_coli_hs/index.shtml</a>).</p>c<p>Considering the complete genome of enteropathogenic strain E2348/69 (phylogenetic group B2) (<a href="http://www.sanger.ac.uk/Projects/Escherichia_Shigella/" target="_blank">http://www.sanger.ac.uk/Projects/Escherichia_Shigella/</a>). This strain is not virulent (0 of 10 mice killed) in the mouse model of extraintestinal virulence <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000344#pgen.1000344-Johnson2" target="_blank">[32]</a>.</p>d<p>Genes on the virulence plasmid <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000344#pgen.1000344-Buchrieser1" target="_blank">[56]</a>, not detailed in the subsequent columns.</p>