Additional file 1.

Supplementary Methods, Figures S1 to S4, Tables S1 to S5, and Supplementary References. Supplementary Methods: preparation of whole cellular, membrane and extracellular proteins, two-dimensional gel electrophoresis and image analysis, and metabolite abbreviations in Figure 4. Figure S1: growth curves of E. coli B strains (REL606 and BL21(DE3) and K-12 strains (MG1655 and W3110) in complex LB medium and minimal R/2 medium supplemented with 10 g/l glucose. Figure S2: total cellular, outer membrane, and extracellular proteomes of the E. coli strains. Figure S3: phenotype microarray comparison of E. coli B REL606 and K-12 MG1655. Figure S4: phylogenetic position of two T2S systems in E. coli B REL606. Table S1: pseudogene comparison between E. coli B REL606 and K-12 MG1655. Table S2: genes that were highly expressed at both the exponential and stationary growth phases during growth of E. coli B REL606 and K-12 MG1655 in LB medium. Table S3: proteins exhibiting significant quantitative differences between E. coli B and K-12 strains. Table S4: metabolic reactions modified in the metabolic network model for E. coli B REL606 compared to the model for E. coli K-12 MG1655. Table S5: phenotypic differences of E. coli B REL606 and K-12 MG1655 in PM1 and PM2 and in silico predictions of cell growth on each carbon source. Supplementary References.

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Yoon et al. Genome Biology 2012 13:R37   doi:10.1186/gb-2012-13-5-r37