Supplementary Material (ESI) for Molecular BioSystems This journal is © The Royal Society of Chemistry 2009 The list of genes that are expressed in all the growth conditions but predicted as non-essential in all. acea isocitrate lyase acna aconitate hydratase 1 acnb bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase ahpc alkyl hydroperoxide reductase, C22 subunit ansa cytoplasmic L-asparaginase I argg argininosuccinate synthetase arop aromatic amino acid transporter aspc aspartate aminotransferase, PLP-dependent bcr bicyclomycin/multidrug efflux system bgla 6-phospho-beta-glucosidase A bglx beta-D-glucoside glucohydrolase, periplasmic brnq predicted branched chain amino acid transporter (LIV-II) cyoa cytochrome o ubiquinol oxidase subunit II cysk cysteine synthase A, O-acetylserine sulfhydrolase A subunit cytr DNA-binding transcriptional dual regulator dam DNA adenine methylase dcp dipeptidyl carboxypeptidase II dead ATP-dependent RNA helicase deod purine-nucleoside phosphorylase exox DNA exonuclease X fbaa fructose-bisphosphate aldolase, class II fdog formate dehydrogenase-O, large subunit fhua ferrichrome outer membrane transporter flda flavodoxin 1 fliy cystine transporter subunit galr DNA-binding transcriptional repressor gaty D-tagatose 1,6-bisphosphate aldolase 2, catalytic subunit gatz D-tagatose 1,6-bisphosphate aldolase 2, subunit glgb 1,4-alpha-glucan branching enzyme glna glutamine synthetase glnh glutamine transporter subunit gnd gluconate-6-phosphate dehydrogenase, decarboxylating hisj histidine/lysine/arginine/ornithine transporter subunit hsca DnaK-like molecular chaperone specific for IscU htpx predicted endopeptidase iaaa L-asparaginase ilvb acetolactate synthase I, large subunit kgtp alpha-ketoglutarate transporter lysp lysine transporter mana mannose-6-phosphate isomerase manz mannose-specific enzyme IID component of PTS mdog glucan biosynthesis protein, periplasmic mdoh glucan biosynthesis: glycosyl transferase metq DL-methionine transporter subunit mgsa methylglyoxal synthase mgta magnesium transporter mpra DNA-binding transcriptional repressor of microcin B17 synthesis and multidrug efflux mtld mannitol-1-phosphate dehydrogenase, NAD(P)-binding nagk N-acetyl-D-glucosamine kinase ndh respiratory NADH dehydrogenase 2/cupric reductase oppa oligopeptide transporter subunit pflb pyruvate formate lyase I pncb nicotinate phosphoribosyltransferase potc polyamine transporter subunit prop proline/glycine betaine transporter ptsp fused PTS enzyme: PEP-protein phosphotransferase (enzyme I)/GAF domain containing protein rfag glucosyltransferase I rimj ribosomal-protein-S5-alanine N-acetyltransferase rna ribonuclease I rob DNA-binding transcriptional activator sfsa predicted DNA-binding transcriptional regulator soda superoxide dismutase, Mn spea biosynthetic arginine decarboxylase, PLP-binding sped S-adenosylmethionine decarboxylase tola membrane anchored protein in TolA-TolQ-TolR complex yajo 2-carboxybenzaldehyde reductase, function unknown ybal predicted transporter with NAD(P)-binding Rossmann-fold domain ycdx predicted zinc-binding hydrolase ycfp conserved protein ycge predicted DNA-binding transcriptional regulator ydho predicted lipoprotein yebz predicted inner membrane protein yedi conserved inner membrane protein yghb conserved inner membrane protein yhfa conserved protein ynce conserved protein yrdd predicted DNA topoisomerase