Fig. 1

Genome-scale reconstruction steps and gene comparison. A Workflow of the construction of iHM1533 B All stages of the iHM1533 model construction, with the number of genes, reactions, and metabolites present in the model at each stage. C Origin of all reactions in iHM1533, divided by subsystem. The iHM1533 model is based on a reduced iML1515 model (iML1515-origin), to which reactions were added from 54 models of E. coli/Shigella strains (Reference strains) and the existing EcN model (iDK1463). During curation, additional reactions were added to correct the model and to expand various secondary metabolite biosynthesis pathways (Manual). D Heatmap of gene homology of all 55 strains to EcN. Strains were clustered in four groups: commensal, extraintestinal pathogenic E. coli (ExPEC), intestinal pathogenic E. coli (InPEC), and Shigella. Genes with homology above 80% were deemed homologous (blue) and those below 80% were not (white). The highest number of homologous genes is shared with ExPEC strains, which also has previously been observed by Grozdanov et al. [34], when comparing EcN to 324 non-pathogenic and pathogenic E. coli isolates