Table 2 Predicted attenuators in the genome of E. coli
From: Identification of attenuation and antitermination regulation in prokaryotes
ID | Z-score | Known | Upstream promotera | Geneb |
b4119 | -9.279 | alpha-galactosidase (melA) | ||
b2019 | -7.560 | √ | √ | ATP phosphoribosyltransferase (hisG) |
b3828 | -7.143 | regulator for metE and metH (metR) | ||
b3543 | -7.009 | dipeptide transport system permease protein 1 (dppB) | ||
b4118 | -6.911 | regulator of melibiose operon (melR) | ||
b2425 | -6.168 | √ | thiosulfate binding protein (cysP) | |
b0560 | -5.838 | √ | bacteriophage DNA packaging protein (nohB) | |
b4385 | -5.755 | hypothetical protein (yjjJ) | ||
b3866 | -5.703 | hypothetical protein (yihI) | ||
b0689 | -5.697 | putative pectinase (ybfP) | ||
b1548 | -5.638 | √ | homolog of Qin prophage packaging protein NU1 (nohA) | |
b1825 | -5.573 | √ | hypothetical protein | |
b0611 | -5.528 | RNase I, cleaves phosphodiester bond between any two nucleotides (rna) | ||
b2622 | -5.470 | prophage CP4-57 integrase (intA) | ||
b3066 | -5.002 | DNA biosynthesis; DNA primase (dnaG) | ||
b0654 | -4.844 | glutamate/aspartate transport system permease (gltJ) | ||
b1978 | -4.772 | √ | putative factor | |
b3767 | -4.529 | √ | acetolactate synthase II, large subunit, cryptic, interrupted (ilvG_1) | |
b2119 | -4.518 | √ | hypothetical protein (yehL) | |
b2792 | -4.444 | hypothetical protein | ||
b0902 | -4.443 | √ | pyruvate formate lyase activating enzyme 1 (pflA) | |
b3871 | -4.352 | √ | putative GTP-binding factor (yihK) | |
b2937 | -4.347 | √ | agmatinase (speB) | |
b0939 | -4.300 | putative chaperone (ycbR) | ||
b1431 | -4.280 | √ | hypothetical protein | |
b0890 | -4.275 | cell division protein (ftsK) | ||
b2632 | -4.177 | √ | putative GTP-binding protein (yfjP) | |
b0048 | -4.168 | √ | dihydrofolate reductase type I (folA) | |
b0336 | -4.133 | cytosine permease/transport (codB) | ||
b2517 | -4.076 | √ | hypothetical protein (yfgB) | |
b3438 | -4.018 | regulator of gluconate (gnt) operon (gntR) | ||
b2599 | -3.945 | √ | √ | chorismate mutase-P and prephenate dehydratase (pheA) |
b3671 | -3.923 | √ | √ | acetolactate synthase I, valine-sensitive, large subunit (ilvB) |
b2775 | -3.907 | √ | putative transport protein (yqcE) | |
b2609 | -3.891 | √ | 30S ribosomal subunit protein S16 (rpsP) | |
b3181 | -3.889 | transcription elongation factor: cleaves 3' nucleotide of paused mRNA (greA) | ||
b3983 | -3.861 | √ | 50S ribosomal subunit protein L11 (rplK) | |
b3722 | -3.823 | √ | PTS beta-glucosides enzyme II, cryptic (bglF) | |
b0002 | -3.788 | √ | √ | aspartokinase I, homoserine dehydrogenase I (thrA) |
b0196 | -3.759 | regulator in colanic acid synthesis; interacts with RcsB (rcsF) | ||
b0007 | -3.711 | inner membrane transport protein (yaaJ) | ||
b3513 | -3.694 | putative membrane protein (yhiU) | ||
b3088 | -3.669 | √ | putative transport protein (ygjT) | |
b4178 | -3.630 | √ | hypothetical protein (yjeB) | |
b3752 | -3.573 | √ | ribokinase (rbsK) | |
b2643 | -3.572 | hypothetical protein (yfjX) | ||
b0074 | -3.559 | √ | √ | 2-isopropylmalate synthase (leuA) |
b2096 | -3.530 | √ | tagatose-bisphosphate aldolase 1 (gatY) | |
b0170 | -3.506 | √ | √ | elongation factor EF-Ts (tsf) |
b0610 | -3.506 | √ | regulator of nucleoside diphosphate kinase (rnk) | |
b3813 | -3.503 | √ | DNA-dependent ATPase I and helicase II (uvrD) | |
b1851 | -3.446 | 6-phosphogluconate dehydratase (edd) | ||
b2359 | -3.395 | √ | hypothetical protein | |
b4245 | -3.387 | √ | aspartate carbamoyltransferase, catalytic subunit (pyrB) | |
b4377 | -3.374 | √ | hypothetical protein (yjjU) | |
b3298 | -3.362 | √ | 30S ribosomal subunit protein S13 (rpsM) | |
b0606 | -3.358 | alkyl hydroperoxide reductase, F52a subunit (ahpF) | ||
b0018 | -3.350 | √ | Gef protein interferes with membrane function when in excess (gef) | |
b2958 | -3.329 | hypothetical protein (yggN) | ||
b3822 | -3.303 | ATP-dependent DNA helicase (recQ) | ||
b0241 | -3.292 | outer membrane pore protein E (phoE) | ||
b0680 | -3.260 | glutamine tRNA synthetase (glnS) | ||
b0404 | -3.233 | putative glycoprotein (yajB) | ||
b3337 | -3.232 | √ | hypothetical protein (yheA) | |
b3190 | -3.181 | hypothetical protein (yrbA) | ||
b0860 | -3.147 | arginine 3rd transport system periplasmic binding protein (artJ) | ||
b1922 | -3.115 | √ | flagellar biosynthesis; regulation of flagellar operons (fliA) | |
b2836 | -3.103 | 2-acyl-glycerophospho-ethanolamine acyltransferase; acyl-acyl-carrier protein synthetase (aas) | ||
b3915 | -3.087 | putative transport system permease protein (yiiP) | ||
b3310 | -3.083 | √ | 50S ribosomal subunit protein L14 (rplN) | |
b0119 | -3.018 | hypothetical protein (yacL) | ||
b3748 | -3.005 | D-ribose high-affinity transport system; membrane-associated protein (rbsD) | ||
b2313 | -2.990 | √ | membrane protein required for colicin V production (cvpA) | |
b1352 | -2.967 | √ | hypothetical protein (ydaD) | |
b0441 | -2.961 | putative protease maturation protein (ybaU) | ||
b3161 | -2.947 | tryptophan-specific transport protein (mtr) | ||
b1614 | -2.888 | √ | hypothetical protein (ydgA) | |
b3528 | -2.862 | √ | uptake of C4-dicarboxylic acids (dctA) | |
b2514 | -2.812 | √ | histidine tRNA synthetase (hisS) | |
b3390 | -2.810 | √ | shikimate kinase I (aroK) | |
b1253 | -2.808 | hypothetical protein (yciA) | ||
b2724 | -2.808 | √ | probable small subunit of hydrogenase-3, iron-sulfur protein (part of formate hydrogenlyase (FHL) complex) (hycB) | |
b4242 | -2.806 | Mg2+ transport ATPase, P-type 1 (mgtA) | ||
b0208 | -2.804 | putative transcriptional regulator LYSR-type (yafC) | ||
b1479 | -2.790 | √ | NAD-linked malate dehydrogenase (malic enzyme) (sfcA) | |
b1838 | -2.749 | √ | protein phosphatase 1 modulates phosphoproteins, signals protein misfolding (pphA) | |
b0189 | -2.741 | √ | hypothetical protein (yaeO) | |
b1264 | -2.717 | √ | anthranilate synthase component I (trpE) | |
b4313 | -2.706 | √ | recombinase involved in phase variation; regulator for fimA (fimE) | |
b3573 | -2.691 | hypothetical protein (yiaI) | ||
b3642 | -2.675 | √ | orotate phosphoribosyltransferase (pyrE) | |
b0034 | -2.646 | √ | transcriptional regulator of cai operon (caiF) | |
b2176 | -2.635 | hypothetical protein (rtn) | ||
b1769 | -2.618 | putative transport protein (ydjE) | ||
b1561 | -2.605 | hypothetical protein (rem) | ||
b1050 | -2.605 | hypothetical protein (yceK) | ||
b2643 | -2.604 | hypothetical protein (yfjX) | ||
b0248 | -2.604 | hypothetical protein (yafX) | ||
b4278 | -2.591 | √ | IS4 hypothetical protein (yi41) | |
b3560 | -2.583 | glycine tRNA synthetase, alpha subunit (glyQ) | ||
b3723 | -2.565 | √ | √ | positive regulation of bgl operon (bglG) |
b1689 | -2.560 | √ | hypothetical protein | |
b3632 | -2.528 | √ | lipopolysaccharide core biosynthesis (rfaQ) | |
b1404 | -2.521 | √ | IS30 transposase (tra8_2) | |
b2014 | -2.519 | √ | putative amino acid/amine transport protein (yeeF) | |
b2924 | -2.487 | putative transport protein (yggB) | ||
b0070 | -2.433 | √ | putative transport protein (yabM) | |
b4037 | -2.409 | √ | periplasmic protein of mal regulon (malM) | |
b2359 | -2.405 | hypothetical protein | ||
b3571 | -2.393 | √ | alpha-amylase (malS) | |
b4082 | -2.370 | putative membrane protein (yjcR) | ||
b0174 | -2.360 | √ | hypothetical protein (yaeS) | |
b4392 | -2.359 | soluble lytic murein transglycosylase (slt) | ||
b2938 | -2.347 | √ | biosynthetic arginine decarboxylase (speA) | |
b2443 | -2.331 | √ | hypothetical protein | |
b4090 | -2.296 | √ | ribose 5-phosphate isomerase B (rpiB) | |
b2140 | -2.289 | √ | putative regulator protein (yohI) | |
b1861 | -2.274 | √ | Holliday junction helicase subunit B (ruvA) | |
b3196 | -2.274 | √ | hypothetical protein (yrbG) | |
b3054 | -2.268 | hypothetical protein (ygiF) | ||
b1761 | -2.252 | NADP-specific glutamate dehydrogenase (gdhA) | ||
b0763 | -2.248 | √ | molybdate-binding periplasmic protein; permease (modA) | |
b0909 | -2.234 | putative heat shock protein (ycaL) | ||
b3954 | -2.233 | √ | putative ARAC-type regulatory protein (yijO) | |
b3440 | -2.232 | √ | putative regulator (yhhX) | |
b3074 | -2.225 | putative tRNA synthetase (ygjH) | ||
b0605 | -2.218 | √ | alkyl hydroperoxide reductase, C22 subunit; detoxification of hydroperoxides (ahpC) | |
b1053 | -2.218 | putative transport protein (yceE) | ||
b1284 | -2.210 | √ | putative DEOR-type transcriptional regulator | |
b0068 | -2.206 | thiamin-binding periplasmic protein (tbpA) | ||
b0681 | -2.204 | hypothetical protein (ybfM) | ||
b2150 | -2.158 | √ | galactose-binding transport protein; receptor for galactose taxis (mglB) | |
b3349 | -2.153 | √ | FKBP-type peptidyl-prolyl cis-trans isomerase (rotamase) (slyD) | |
b2298 | -2.148 | putative S-transferase (yfcC) | ||
b0554 | -2.133 | √ | hypothetical protein (ybcR) | |
b1778 | -2.121 | hypothetical protein (yeaA) | ||
b1829 | -2.092 | √ | heat shock protein, integral membrane protein (htpX) | |
b2685 | -2.084 | multidrug resistance secretion protein (emrA) | ||
b2456 | -2.069 | detox protein (cchB) | ||
b4284 | -2.067 | √ | IS30 transposase (tra8_3) | |
b1002 | -2.064 | √ | periplasmic glucose-1-phosphatase (agp) | |
b0854 | -2.059 | √ | periplasmic putrescine-binding protein; permease protein (potF) | |
b1368 | -2.051 | putative alpha helix protein | ||
b3088 | -2.048 | √ | putative transport protein (ygjT) | |
b0347 | -2.019 | √ | 3-(3-hydroxyphenyl)propionate hydroxylase (mhpA) | |
b1663 | -2.018 | √ | putative transport protein (ydhE) |