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

aFunctions 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.bConsidering the complete genome of the strain HS (phylogenetic group A). (http://msc.jcvi.org/e_coli_and_shigella/escherichia_coli_hs/index.shtml).cConsidering 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].dGenes on the virulence plasmid [56], not detailed in the subsequent columns.