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Table 2 List of clones containing with -35 and -10 conservative sequences or TF binding sequences

From: Identification of stress-responsive transcription factors with protein-bound Escherichia coli genomic DNA libraries

Gene names Clone ID Library Encoded function Insert length (bp) TFBS
aor 141 TC Aldehyde ferredoxin oxidoreductase 279 Sigma70
araH 28 GA l-arabinose ABC transporter permease 167 Sigma70, DnaA
arcB 47 AC Sensor histidine kinase 258 Sigma 70, Ihf
argB 80 AC Acetylglutamate kinase 225 Sigma70, ArgR2, Ihf
arsB 65, 85, 108, 114 AG, CA CT, TT Arsenite/antimonite:H(+) antiporter 320 Sigma70
bglH 72 AT Carbohydrate-specific outer membrane porin 244 Sigma70, PurR
bsl78 107 CT DNA (cytosine-5-)-methyltransferase 218 Sigma 70
cas1e 18 GG Type I-E CRISPR-associated protein 186 Sigma70, RpoS17
casA 37 GG CRISPR system Cascade subunit 158 Sigma70, RpoS17
chbC 73 AT N,N’-diacetylchitobiose-specific PTS enzyme IIC 158 Fur, RpoD17
chbG 70, 91 AT Chitin disaccharide deacetylase 157 Sigma70
clk_1237 177 TA ADP-ribosylglycohydrolase family protein 124 Sigma70
ctk 93 CA DUF4297 domain-containing protein 135 Sigma70, RpoD15, metJ
ctpA3 144 TC Carboxyl-terminal-processing peptidase 3, chloroplastic 158 Sigma70
cydD 145 TC Cysteine/glutathione ABC transporter permease/ATP-binding protein 167 Sigma70
dgc 122 TT Diguanylate cyclases 105 Sigma70, RpoD17
dtpD 137 TC Dipeptide permease 213 Sigma70, LexA
eamA 74 AT Cysteine/O-acetylserine exporter EamA 184 Sigma70
ecm18 150 TG Class I SAM-dependent methyltransferase 270 Sigma70, Crp, SoxS
ef2563 35 GG Selenium-dependent molybdenum hydroxylase system protein 133 Sigma70
egc82 33 GG d-hexose-6-phosphate mutarotase 139 Sigma70
elbB 138 TC Isoprenoid biosynthesis glyoxalase 328 Sigma70, Irp,RpoH2, LexA, ArcA, argR, GlpR:
f0f1 171 TA ATP synthase subunit delta 134 Sigma70
fimZ 165 TA Fimbriae biosynthesis transcriptional regulator 96 Sigma70, PurR, LexA1, LexA2, PurR
frdA 117 TT Fumarate reductase flavoprotein subunit 357 Sigma70
frsA 1, 81 GA, AC Esterase 193 Sigma70
ftr1 3, 4, 11, 12, 13, 14, 15, 21, 27, 57, 62, 95, 97, 110, 111, 112, 126, 154 GA, GC, GT, AC, AG, CG, CT, TC, TG Iron permease 145 Sigma70, RpoD16, MetJ
gaf 6, 24 GA, TC GAF domain-containing protein 262 Ihf
gltT 86 CA Cation:dicarboxylase symporter familytransporter 263 Sigma70, RpoD17, OmpR
gshB 59 AG Glutathione synthase 208 Sigma70, Fis
hcaE 30 GA 3-Phenylpropionate/cinnamic acid dioxygenase subunit alpha 140 Sigma70, DnaA
hemK 147 TC Peptide chain release factor N(5)-glutamate 366 Sigma70
hflC 63 AG Protease modulator 320 Sigma 70
hipA 42 AA Type II toxin-antitoxin system serine/threonine protein kinase toxin 230 Sigma70, RpoD17
hjr 22 GG Holliday junction resolvase 432 RpoD17
hsdR 157 TG Type I restriction-modification system endonuclease 278 Sigma70
IcsA 153 TG Outer membrane protein IcsA autotransporter precursor 196 Sigma70, RpoD17, SoxS
IIA 55 AC PTS mannitol transporter subunit 154 Sigma70, Ihf. ArgR2, RpoD17
kch 53 AC Voltage-gated potassium channel 160 Sigma70, MetJ, RpoH2
kdo 170 TA 3-Deoxy-manno-octulosonate cytidylyltransferase 119 Sigma70, LexA, RpoD18, PurR
kup 155 TG Low affinity potassium transporte 154 Sigma70
lpfC 136, 178 TC, TA Fimbrial biogenesis outer membrane usher protein 155 Sigma70
maaFP003_1916 31 GA Si-specific NAD(P) (+) transhydrogenase 381 Sigma70
maeB 94, 116 CA, TT NADP-dependent oxaloacetate-decarboxylating malate dehydrogenase 121 Sigma, RpoD17, ArgR
mcrB 39 GG 5-Methylcytosine-specific restriction enzyme B 128 Sigma70, RpoD17, Irp, Fnr, NagC
mhpR 127 TC DNA-binding transcriptional activator 284 Sigma70, RpoD17, ArgR, ArcA
mnmC 69 AT 5-Methylaminomethyl-2-thiouridine biosynthesis bifunctional protein 182 Sigma70
motA 9 GC Flagellar motor stator protein 98 98 FliA, MotAB, CheAW, CpxR
msyB 120 TT Acidic protein 308 Sigma70, SoxS
mukF 20 GG Chromosome partition protein 123 Sigma70, RpoD17, Irp, RpoH2, Fnr, NagC
narG 159 TG Nitrate reductase subunit alpha 154 Sigma70, ArgR
narI 10 GC Respiratory nitrate reductase subunit gamma 195 195 Sigma70, Crp
nikC 45 AA Nickel ABC transporter permease subunit 164 Sigma70, RpoD16
nrdD 175 TA Anaerobic ribonucleoside-triphosphate reductase 350 Sigma70
nuoE 158 TG NADH-quinone oxidoreductase subunit NuoE 222 Sigma70, Crp
pntA 8, 50 GA Si-specific NAD(P) transhydrogenase 415 Sigma70
rase 56 AC 4-Hydroxybenzoate octaprenyltransfe 178 Sigma, PurR
rayT 88 CA REP-associated tyrosine transposase 248 Sigma70
rep 139 TC ATP-dependent DNA helicase Rep 185 Sigma70
rpoS 156 TG RNA polymerase sigma factor 315 Sigma70, Crp
rppH 169 TA RNA pyrophosphohydrolase 396 Sigma70, NarP
rrl 61 AG 23S ribosomal RNA 153 Crp, RpoD15
sanA 67 AT Outer membrane permeability protein 193 Sigma 70
sdr 149 TG Short-chain dehydrogenase 99 Sigma70
secA 167 TA Preprotein translocase subunit SecA 161 Sigma70, RpoD17, Ihf
sgr 132 TC Helix-turn-helix domain-containing protein 199 Sigma70, ArgR2
speF 90 CA Ornithine decarboxylase SpeF 128 Sigma70
spy 105 CT ATP-independent periplasmic protein-refolding chaperone 233 Ihf, Fis, lrp,
tesB 173 TA Acyl-CoA thioesterase II 133 Sigma70, RpoD16
thiP 99 CT Thiamine/thiamine pyrophosphate ABC transporter permease 210 Sigma70, OmpR
tolC 115 TT Outer membrane channel protein 128 ArgR
trpS/pgp 123 TT Tryptophan–tRNA ligase Phosphoglycolate phosphatase 115 Sigma70
tyrR 134 TC Transcriptional regulator 147 RpoD19, RpoD17, Crp, OmpR, MetR
ucpA 100 CT SDR family oxidoreductase 133 Sigma70, Fnr
ugdH 121 TT UDP-glucose 6-dehydrogenase 294 Sigma70, FlhCD, RpoH2, RpoD17, Fnr, lrp
uhpC 16 GG MFS transporter family glucose-6-phosphate receptor 174 Sigma70, ArgR
wbbI 5, 29 GA Beta-1,6-galactofuranosyltransferase 200 Sigma70
wcaL 129 TC Colanic acid biosynthesis glycosyltransferase 290 Sigma70
weel 24, 75 GT Beta-1,6-galactofuranosyltransferase 217 Sigma70, RpoD17, RpoD16,RpoD17,RpoD17
wzc 109 CT Tyrosine-protein kinase 179 Sigma70
ybaT 89 CA Amino acid permease 171 ArgR2, Ihf, ArcA
ybjX 49 AC DUF535 domain-containing protein YbjX 145 Sigma70
ycbV 148 TG Putative fimbrial-like adhesin protein 110 Sigma70, Crp, RpoD15, PhoB, RpoD17, lrp
ychE 131 TC NAAT family transporter 258 Sigma70, RpoD16, lrp, SoxS, TyrR, GlpR, RpoD18
ydhW 23, 25, 40 GT Oxidoreductase 183 Sigma70
ydiV 52 AC EAL domain-containing protein bacteria 241 Sigma70, Crp
yeaW 101 CT Carnitine monooxygenase subunit 179 Sigma 70
yedE/fdhT 48 AC Selenium metabolism membrane protein 110 Sigma70
yeeJ 119 TT Inverse autotransporter adhesin 182 Sigma70
yeiH 135 TC YeiH family putative sulfate export transporter 114 Sigma70, OxyR, arcA, Fnr, RpoD18, TyrR, Fnr, DeoR, Ihf, ArgR2
yfeX 54 AC Porphyrinogen peroxidase 167 Sigma70
yhdP 46 AA AsmA2 domain-containing protein 200 Sigma70
yidR 125 TC DUF3748 domain-containing galacturonate catabolism protein 174 Sigma70
yihG 151 TG Putative acyltransferase 186 Sigma70
yneE 98 CG Bestrophin family inner membrane protein 120 Sigma70
ypfG 64 AG DUF1176 domain-containing protein 328 Sigma70, RpoH3
  26 GT Hypothetical protein 211 Sigma 70, ArgR2, Crp
  152 TG Non-coding, Pseudo genes 186 Sigma70, Fis, Fnr, LexA
  161 TG Unknown 626 Sigma70