Supplementary Material (ESI) for Molecular BioSystems This journal is © The Royal Society of Chemistry 2009 The list of genes that are predicted to be essential in all the studied growth conditions accd acetyl-CoA carboxylase, beta (carboxyltranferase) subunit acpp acyl carrier protein (ACP) alas alanyl-tRNA synthetase arca DNA-binding response regulator in two-component regulatory system with ArcB or CpxA atpd F1 sector of membrane-bound ATP synthase, beta subunit atpg F1 sector of membrane-bound ATP synthase, gamma subunit can carbonic anhydrase clpa ATPase and specificity subunit of ClpA-ClpP ATP-dependent serine protease, chaperone activity clpb protein disaggregation chaperone clpp proteolytic subunit of ClpA-ClpP and ClpX-ClpP ATP-dependent serine proteases clpx ATPase and specificity subunit of ClpX-ClpP ATP-dependent serine protease cora magnesium/nickel/cobalt transporter cpxr DNA-binding response regulator in two-component regulatory system with CpxA cyaa adenylate cyclase daca D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5) dapd 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase degq serine endoprotease, periplasmic dnaa chromosomal replication initiator protein DnaA, DNA-binding transcriptional dual regulator dnae DNA polymerase III alpha subunit dnag DNA primase dnax DNA polymerase III/DNA elongation factor III, tau and gamma subunits eno enolase era membrane-associated, 16S rRNA-binding GTPase fabd malonyl-CoA-[acyl-carrier-protein] transacylase fbp fructose-1,6-bisphosphatase I fmt 10-formyltetrahydrofolate:L-methionyl-tRNA(fMet) N-formyltransferase ftsi transpeptidase involved in septal peptidoglycan synthesis (penicillin-binding protein 3) ftsz GTP-binding tubulin-like cell division protein glnd uridylyltransferase gph phosphoglycolate phosphatase gpp guanosine pentaphosphatase/exopolyphosphatase gpsa glycerol-3-phosphate dehydrogenase (NAD+) gshb glutathione synthetase hemd uroporphyrinogen III synthase hemn coproporphyrinogen III oxidase, SAM and NAD(P)H dependent, oxygen-independent hemx predicted uroporphyrinogen III methylase hflc modulator for HflB protease specific for phage lambda cII repressor hflk modulator for HflB protease specific for phage lambda cII repressor hfq HF-I, host factor for RNA phage Q beta replication hola DNA polymerase III, delta subunit htpg molecular chaperone HSP90 family hupa HU, DNA-binding transcriptional regulator, alpha subunit inta CP4-57 prophage; integrase ispg 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase lepa GTP-binding membrane protein lgt phosphatidylglycerol-prolipoprotein diacylglyceryl transferase lola chaperone for lipoproteins lpxd UDP-3-O-(3-hydroxymyristoyl)-glucosamine N-acyltransferase mdh malate dehydrogenase, NAD(P)-binding metk methionine adenosyltransferase 1 miaa delta(2)-isopentenylpyrophosphate tRNA-adenosine transferase mltd predicted membrane-bound lytic murein transglycosylase D mraw S-adenosyl-dependent methyltransferase activity on membrane-located substrates mrp antiporter inner membrane protein mura UDP-N-acetylglucosamine 1-carboxyvinyltransferase murb UDP-N-acetylenolpyruvoylglucosamine reductase, FAD-binding nagz beta N-acetyl-glucosaminidase nlpd predicted outer membrane lipoprotein obge GTPase involved in cell partioning and DNA repair ompa outer membrane protein A (3a;II*;G;d) ompf outer membrane porin 1a (Ia;b;F) panc pantothenate synthetase pepa aminopeptidase A, a cyteinylglycinase pepn aminopeptidase N phes phenylalanine tRNA synthetase, alpha subunit phet phenylalanine tRNA synthetase, beta subunit pnp polynucleotide phosphorylase/polyadenylase pola DNA polymerase I ppid peptidyl-prolyl cis-trans isomerase (rotamase D) ppx exopolyphosphatase pqib paraquat-inducible protein B prfc peptide chain release factor RF-3 pstb phosphate transporter subunit rlpb minor lipoprotein rlud 23S rRNA pseudouridine synthase rng ribonuclease G rnr exoribonuclease R, RNase R rpla 50S ribosomal subunit protein L1 rple 50S ribosomal subunit protein L5 rplp 50S ribosomal subunit protein L16 rpls 50S ribosomal subunit protein L19 rpod RNA polymerase, sigma 70 (sigma D) factor rpoh RNA polymerase, sigma 32 (sigma H) factor rpoz RNA polymerase, omega subunit rpsa 30S ribosomal subunit protein S1 rpsb 30S ribosomal subunit protein S2 rpsc 30S ribosomal subunit protein S3 rpsd 30S ribosomal subunit protein S4 rpsg 30S ribosomal subunit protein S7 rpsn 30S ribosomal subunit protein S14 rpsp 30S ribosomal subunit protein S16 rsea anti-sigma factor rseb anti-sigma factor seca preprotein translocase subunit, ATPase secd SecYEG protein translocase auxillary subunit sece preprotein translocase membrane subunit secf SecYEG protein translocase auxillary subunit serc 3-phosphoserine/phosphohydroxythreonine aminotransferase spot bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase sppa protease IV (signal peptide peptidase) tgt tRNA-guanine transglycosylase thrb homoserine kinase tolb periplasmic protein tolq membrane spanning protein in TolA-TolQ-TolR complex topa DNA topoisomerase I, omega subunit tpia triosephosphate isomerase trmd tRNA (guanine-1-)-methyltransferase tufa protein chain elongation factor EF-Tu (duplicate of tufB) tufb protein chain elongation factor EF-Tu (duplicate of tufA) ubig bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase uvrc excinuclease UvrABC, endonuclease subunit yacf conserved protein ybex predicteed ion transport ybez predicted protein with nucleoside triphosphate hydrolase domain ybgf predicted protein ycca inner membrane protein ycfd conserved protein ycim conserved protein yeba predicted peptidase yejm predicted hydrolase, inner membrane yfga conserved protein yfio ygfz predicted folate-dependent regulatory protein yhbc conserved protein yiha GTP-binding protein