B number Gene name Regulator role mRNA intensity mRNA present # of tryptic peptides predicted Protein detected - total list Gene description Functional category b0012 htgA + 149 P 11 positive regulator for sigma 32 heat shock promoters Cell processes b0020 nhaR + 645 P 13 transcriptional activator of nhaA Cell processes b0034 caiF + 813 P 9 transcriptional regulator of cai operon Metabolism of small molecules b0064 araC +/- 704 P 10 transcriptional regulator for ara operon Metabolism of small molecules b0076 leuO + 158 P 15 probable transcriptional activator for leuABCD operon Metabolism of small molecules b0080 fruR +/- 510 P 14 P transcriptional repressor of fru operon and others Metabolism of small molecules b0113 pdhR - 311 P 8 transcriptional regulator for pyruvate dehydrogenase complex Metabolism of small molecules b0240 crl + 7201 P 8 P transcriptional regulator of cryptic csgA gene for curli surface fibers Structural elements b0254 perR - 174 P 14 putative transcriptional regulator LYSR-type Miscellaneous b0313 betI - 2262 P 13 probably transcriptional repressor of bet genes Cell processes b0330 prpR + 221 A 23 regulator for prp operon Miscellaneous b0338 cynR +/- 272 P 17 cyn operon positive regulator Metabolism of small molecules b0345 lacI - 324 P 16 transcriptional repressor of the lac operon Metabolism of small molecules b0346 mhpR + 1278 P 16 transcriptional regulator for mhp operon Miscellaneous b0399 phoB + 399 P 9 positive response regulator for pho regulon, sensor is PhoR (or CreC) Global functions b0435 bolA + 2088 P 5 P possible regulator of murein genes Structural elements b0464 acrR - 260 P 13 acrAB operon repressor Cell processes b0535 fimZ + 54 A 11 fimbrial Z protein; probable signal transducer Structural elements b0564 appY +/- 98 P 15 regulatory protein affecting appA and other genes Metabolism of small molecules b0566 envY + 49 A 14 envelope protein; thermoregulation of porin biosynthesis Structural elements b0620 citB + 320 P 10 sequence similarity to Shigella regulator Miscellaneous b0623 cspE + 6086 P 5 P cold shock protein Miscellaneous b0676 nagC - 799 P 24 transcriptional repressor of nag (N-acetylglucosamine) operon Metabolism of small molecules b0683 fur - 4618 P 8 P negative regulator Global functions b0694 kdpE + 643 P 15 P regulator of kdp operon (transcriptional effector) Global functions b0730 farR - 345 P 10 transcriptional regulator of succinylCoA synthetase operon Metabolism of small molecules b0761 modE - 380 P 10 molybdate uptake regulatory protein Cell processes b0840 deoR - 509 P 9 transcriptional repressor for deo operon, tsx, nupG Metabolism of small molecules b0880 cspD + 17935 P 2 P cold shock protein Miscellaneous b0889 lrp +/- 3450 P 9 P regulator for leucine (or lrp) regulon and high-affinity branched-chain amino acid transport system Metabolism of small molecules b0912 himD +/- 10452 P 4 integration host factor (IHF), beta subunit; site-specific recombination Macromolecule metabolism b0990 cspG + 311 P 5 P homolog of Salmonella cold shock protein Miscellaneous b0995 torR + 444 P 10 response transcriptional regulator for torA (sensor TorS) Metabolism of small molecules b1004 wrbA - 6589 P 9 P trp repressor binding protein; affects association of trp repressor and operator Metabolism of small molecules b1014 putA - 358 P 57 P proline dehydrogenase, P5C dehydrogenase Metabolism of small molecules b1040 csgD + 469 P 15 putative 2-component transcriptional regulator for 2nd curli operon Miscellaneous b1130 phoP + 6704 P 11 P transcriptional regulatory protein Global functions b1187 fadR +/- 581 P 14 negative regulator for fad regulon, and positive activator of fabA Metabolism of small molecules b1221 narL +/- 2563 P 9 P pleiotrophic regulation of anaerobic respiration: response regulator for nar, frd, dms and tor genes Metabolism of small molecules b1237 hns - 34541 P 7 P DNA-binding protein HLP-II (HU, BH2, HD, NS); pleiotropic regulator Macromolecule metabolism b1275 cysB +/- 566 P 16 P positive transcriptional regulator for cysteine regulon Metabolism of small molecules b1303 pspF + 310 P 15 psp operon transcriptional activator Extrachromosomal b1306 pspC + 525 P 5 phage shock protein: activates phage shock-protein expression Extrachromosomal b1323 tyrR +/- 662 P 27 transcriptional regulation of aroF, aroG, tyrA and aromatic amino acid transport Cell processes b1334 fnr +/- 107 A 4 transcriptional regulation of aerobic, anaerobic respiration, osmotic balance Global functions b1384 feaR + 223 P 12 regulatory protein for 2-phenylethylamine catabolism Miscellaneous b1507 hipA - 373 P 25 persistence to inhibition of murein or DNA biosynthesis, DNA-binding regulator Structural elements b1508 hipB - 688 P 5 persistence to inhibition of murein or DNA biosynthesis; regulatory protein Structural elements b1530 marR - 553 P 5 multiple antibiotic resistance protein; repressor of mar operon Cell processes b1531 marA + 1163 P 8 multiple antibiotic resistance; transcriptional activator of defense systems Cell processes b1552 cspI + 40 A 5 cold shock-like protein Miscellaneous b1557 cspB + 30 A 5 cold shock protein; may affect transcription Cell processes b1558 cspF + 36 A 4 cold shock protein Miscellaneous b1569 dicC - 114 P 7 regulator of dicB Cell processes b1570 dicA - 1308 P 6 regulator of dicB Cell processes b1594 mlc - 288 P 19 putative NAGC-like transcriptional regulator Open reading frames b1608 rstA + 1968 P 13 P response transcriptional regulatory protein (RstB sensor) Miscellaneous b1618 uidR - 474 P 11 repressor for uid operon Metabolism of small molecules b1620 malI - 199 P 17 repressor of malX and Y genes Metabolism of small molecules b1642 slyA + 3141 P 7 P transcriptional regulator for cryptic hemolysin Cell processes b1658 purR - 1323 P 18 P transcriptional repressor for pur regulon, glyA, glnB, prsA, speA Metabolism of small molecules b1712 himA +/- 4469 P 6 P integration host factor (IHF), alpha subunit; site specific recombination Macromolecule metabolism b1735 celD - 97 A 15 negative transcriptional regulator of cel operon Metabolism of small molecules b1823 cspC + 30711 P 5 P cold shock protein Miscellaneous b1891 flhC + 231 P 6 regulator of flagellar biosynthesis acting on class 2 operons; transcription initiation factor Structural elements b1892 flhD + 810 P 7 regulator of flagellar biosynthesis, acting on class 2 operons; transcriptional initiation factor Structural elements b1914 uvrY + 2055 P 12 putative 2-component transcriptional regulator Miscellaneous b1916 sdiA + 241 P 10 transcriptional regulator of ftsQAZ gene cluster Cell processes b1951 rcsA + 86 A 8 positive regulator for ctr capsule biosynthesis, positive transcription factor Structural elements b1987 cbl +/- 501 P 19 P transcriptional regulator cys regulon; accessory regulatory circuit affecting cysM Metabolism of small molecules b1988 nac +/- 148 A 10 nitrogen assimilation control protein Metabolism of small molecules b2079 baeR + 868 P 15 transcriptional response regulatory protein (sensor BaeS) Global functions b2082 ogrK + 708 P 4 prophage P2 ogr protein Extrachromosomal b2090 gatR_2 - 3175 P 5 split galactitol utilization operon repressor, fragment 2 Metabolism of small molecules b2151 galS - 313 P 19 mgl repressor, galactose operon inducer Metabolism of small molecules b2193 narP +/- 878 P 9 nitrate/nitrite response regulator (sensor NarQ) Metabolism of small molecules b2213 ada +/- 418 P 22 O6-methylguanine-DNA methyltransferase; transcription activator/repressor Macromolecule metabolism b2217 rcsB + 3714 P 9 P positive response regulator for colanic capsule biosynthesis, (sensor, RcsC) Structural elements b2220 atoC + 388 P 25 response regulator of ato, ornithine decarboxylase antizyme (sensor ATOS) Metabolism of small molecules b2289 lrhA - 919 P 9 LysR homologue which modulates SprE(RssB) activity Metabolism of small molecules b2364 dsdC +/- 125 A 12 D-serine dehydratase (deaminase) transcriptional activator Metabolism of small molecules b2369 evgA + 1039 P 11 putative positive transcription regulator (sensor EvgS) Miscellaneous b2405 xapR + 161 A 14 regulator for xapA Metabolism of small molecules b2479 gcvR - 3742 P 7 P transcriptional regulation of gcv operon Metabolism of small molecules b2491 hyfR + 118 A 30 putative 2-component regulator, interaction with sigma 54 Miscellaneous b2624 alpA + 16 A 3 prophage CP4-57 regulatory protein alpA Extrachromosomal b2684 emrR - 4437 P 8 P regulator of plasmid mcrB operon (microcin B17 synthesis) Extrachromosomal b2706 gutM + 40 A 5 glucitol operon activator Metabolism of small molecules b2707 srlR - 560 P 12 regulator for gut (srl), glucitol operon Metabolism of small molecules b2712 hypF - 229 A 23 transcriptional regulatory protein Metabolism of small molecules b2714 ascG - 443 P 15 ascBF operon repressor Metabolism of small molecules b2725 hycA + 40 A 9 transcriptional repression of hyc and hyp operons Metabolism of small molecules b2731 fhlA + 300 P 35 formate hydrogen-lyase transcriptional activator for fdhF, hyc and hyp operons Metabolism of small molecules b2782 chpA - 680 P 6 probable growth inhibitor, PemK-like, autoregulated Miscellaneous b2805 fucR + 1316 P 10 positive regulator of the fuc operon Metabolism of small molecules b2808 gcvA +/- 413 P 14 positive regulator of gcv operon Metabolism of small molecules b2837 galR - 382 P 16 repressor of galETK operon Metabolism of small molecules b2839 lysR +/- 119 A 12 positive regulator for lys Metabolism of small molecules b2916 iciA +/- 302 P 12 P replication initiation inhibitor, binds to 13-mers at oriC Macromolecule metabolism b2980 glcC + 1150 P 13 transcriptional activator for glc operon Metabolism of small molecules b2991 hybF - 176 A 4 may modulate levels of hydrogenease-2 Metabolism of small molecules b3075 ebgR - 412 P 16 regulator of ebg operon Metabolism of small molecules b3094 exuR - 1102 P 14 negative regulator of exu regulon, exuT, uxaAC, and uxuB Metabolism of small molecules b3118 tdcA + 31 A 13 transcriptional activator of tdc operon Metabolism of small molecules b3119 tdcR + 16 A 8 threonine dehydratase operon activator protein Metabolism of small molecules b3131 agaR - 989 P 12 putative DEOR-type transcriptional regulator of aga operon Miscellaneous b3188 nlp + 104 A 5 regulatory factor of maltose metabolism; similar to Ner repressor protein of phage Mu Metabolism of small molecules b3237 argR - 1556 P 5 repressor of arg regulon; cer-mediated site specific recombination Metabolism of small molecules b3261 fis +/- 4945 P 2 site-specific DNA inversion stimulation factor; DNA-binding protein; a trans activator for transcription Macromolecule metabolism b3264 envR - 5 A 11 putative transcriptional regulator Miscellaneous b3357 crp +/- 9299 P 13 P cyclic AMP receptor protein Global functions b3405 ompR +/- 1241 P 13 P response regulator (sensor, EnvZ) affecting transcription of ompC and ompF: outer membrane protein synthesis Global functions b3418 malT + 660 P 44 positive regulator of mal regulon Metabolism of small molecules b3423 glpR - 1150 P 11 P repressor of the glp operon Metabolism of small molecules b3438 gntR - 529 P 14 regulator of gluconate (gnt) operon Metabolism of small molecules b3501 arsR - 317 P 6 transcriptional repressor of chromosomal ars operon Cell processes b3556 cspA + 726 P 4 P cold shock protein 7.4, transcriptional activator of hns Cell processes b3569 xylR +/- 231 P 15 putative regulator of xyl operon Miscellaneous b3601 mtlR - 153 P 7 repressor for mtl Metabolism of small molecules b3604 lldR - 462 P 12 transcriptional regulator Metabolism of small molecules b3641 ttk +/- 2228 P 10 P putative transcriptional regulator Miscellaneous b3669 uhpA + 882 P 9 response regulator, positive activator of uhpT transcription (sensor, uhpB) Cell processes b3702 dnaA +/- 889 P 27 P DNA biosynthesis; initiation of chromosome replication; can be transcription regulator Macromolecule metabolism b3724 phoU - 591 P 13 negative regulator for pho regulon and putative enzyme in phosphate metabolism Global functions b3743 asnC +/- 231 P 10 regulator for asnA, asnC and gidA Metabolism of small molecules b3753 rbsR - 294 P 12 regulator for rbs operon Metabolism of small molecules b3763 pssR +/- 903 P 9 regulator of pssA Macromolecule metabolism b3773 ilvY +/- 299 P 11 positive regulator for ilvC Metabolism of small molecules b3800 aslB + 76 A 11 putative arylsulfatase regulator Miscellaneous b3828 metR +/- 631 P 13 regulator for metE and metH Metabolism of small molecules b3842 rfaH + 190 P 8 transcriptional activator affecting biosynthesis of lipopolysaccharide core, F pilin, and haemolysin Macromolecule metabolism b3868 glnG +/- 451 A 22 P response regulator for gln (sensor glnL) (nitrogen regulator I, NRI) Metabolism of small molecules b3897 frvR - 54 A 30 putative frv operon regulatory protein Miscellaneous b3905 rhaS + 130 A 11 positive regulator for rhaBAD operon Metabolism of small molecules b3906 rhaR + 51 A 16 positive regulator for rhaRS operon Metabolism of small molecules b3912 cpxR + 4548 P 8 P transcriptional regulator in 2-component system Miscellaneous b3934 cytR - 886 P 14 regulator for deo operon, udp, cdd, tsx, nupC, and nupG Global functions b3938 metJ - 2490 P 4 P repressor of all met genes but metF Metabolism of small molecules b3961 oxyR +/- 566 P 15 P activator, hydrogen peroxide-inducible genes Global functions b3973 birA - 262 P 16 biotin-[acetylCoA carboxylase] holoenzyme synthetase and biotin operon repressor Metabolism of small molecules b4004 hydG + 260 P 19 response regulator of hydrogenase 3 activity (sensor HydH) Metabolism of small molecules b4018 iclR - 316 P 15 repressor of aceBA operon Metabolism of small molecules b4043 lexA - 1002 P 10 regulator for SOS(lexA) regulon Global functions b4062 soxS + 1677 P 4 regulation of superoxide response regulon Global functions b4063 soxR + 157 A 8 redox-sensing activator of soxS Global functions b4089 rpiR - 434 P 11 transcriptional repressor of rpiB expression Metabolism of small molecules b4102 phnF - 41 A 13 putative transcriptional regulator Miscellaneous b4113 basR + 591 P 6 transcriptional regulatory protein, member of 2-component regulatory system, Macromolecule metabolism b4116 adiY + 9 A 12 putative ARAC-type regulatory protein Miscellaneous b4118 melR + 145 A 15 regulator of melibiose operon Metabolism of small molecules b4133 cadC + 40 A 19 transcriptional activator of cad operon Metabolism of small molecules b4225 chpB - 546 P 3 probable growth inhibitor, PemK-like, autoregulated Miscellaneous b4241 treR - 175 A 15 repressor of treA,B,C Cell processes b4300 sgcR - 52 A 13 putative DEOR-type transcriptional regulator Miscellaneous b4324 uxuR - 232 A 12 regulator for uxu operon Metabolism of small molecules b4390 nadR - 912 P 23 probable nadAB transcriptional regulator Metabolism of small molecules b4393 trpR - 591 P 6 regulator for trp operon and aroH; trp aporepressor Metabolism of small molecules b4396 rob + 1097 P 11 P right origin-binding protein Macromolecule metabolism b4398 creB + 437 P 9 catabolic regulation response regulator Global functions b4401 arcA +/- 2126 P 11 P negative response regulator of genes in aerobic pathways, (sensors, ArcB and CpxA) Global functions Known E. coli transcriptional regulators as defined by Perez-Rueda and Collado-Vides (2000). This list was matched against the list of E. coli proteins detected by HPLC-MS/MS. Annotation information was taken from the E.coli Entry Point database. The annotation in the database is based on Blattner et al (1997) with some updates made where necessary. Functional categories are assigned as defined by Riley and Labedan (1996). Regulator role according to Perez-Rueda and Collado-Vides (2000): activator (+), repressor (-), and dual-action regulator (+/-).