Table 1 Predicted attenuators in the genome of B. subtilis
From: Identification of attenuation and antitermination regulation in prokaryotes
ID | Z-score | Known | Upstream promotera | Geneb |
BS0929 | -8.895 | √ | glycerol-3-phosphate dehydrogenase (glpD) | |
BS2825 | -8.473 | √ | √ | acetolactate synthase (acetohydroxy-acid synthase) (large subunit) (ilvB) |
BS1310 | -6.836 | similar to chaperonin (ykkC) | ||
BS0983 | -6.733 | √ | hypothetical protein (yhaW) | |
BS3920 | -6.468 | √ | √ | PTS beta-glucoside-specific enzyme IIABC component (bglP) |
BS1257 | -6.332 | RNA polymerase PBSX sigma factor-like (xpf) | ||
BS2733 | -6.238 | √ | alanyl-tRNA synthetase (alaS) | |
BS0013 | -6.126 | √ | √ | seryl-tRNA synthetase (serS) |
BS2184 | -5.942 | √ | hypothetical protein (yphP) | |
BS3966 | -5.840 | √ | hypothetical protein (iolD) | |
BS2749 | -5.839 | √ | histidyl-tRNA synthetase (hisS) | |
BS2520 | -5.815 | √ | √ | glycyl-tRNA synthetase (alpha subunit) (glyQ) |
BS3396 | -5.767 | √ | √ | similar to amino acid permease (yvbW) |
BS0215 | -5.526 | √ | √ | glycerol-3-phosphate permease (glpT) |
BS2255 | -5.344 | hypothetical protein (ypiA) | ||
BS2600 | -5.342 | similar to phage-related protein (yqbK) | ||
BS1544 | -5.239 | √ | √ | isoleucyl-tRNA synthetase (ileS) |
BS3710 | -5.196 | √ | CTP synthetase (ctrA) | |
BS3895 | -5.191 | √ | similar to pyrimidine nucleoside transport protein (yxjA) | |
BS3798 | -5.164 | √ | √ | PTS sucrose-specific enzyme IIBC component (sacP) |
BS2614 | -5.152 | √ | hypothetical protein (yqaQ) | |
BS2484 | -5.148 | √ | similar to 5-formyltetrahydrofolate cyclo-ligase (yqgN) | |
BS1319 | -5.124 | √ | √ | cobalamin-independent methionine synthase (metC) |
BS2682 | -4.990 | √ | hypothetical protein (yraL) | |
BS3750 | -4.958 | √ | √ | threonyl-tRNA synthetase (thrZ) |
BS0183 | -4.938 | √ | NADH dehydrogenase (subunit 5) (ndhF) | |
BS3440 | -4.890 | √ | √ | levansucrase (sacB) |
BS2715 | -4.841 | √ | similar to formate dehydrogenase (yrhE) | |
BS2204 | -4.819 | √ | √ | xanthine phosphoribosyltransferase (xpt) |
BS2139 | -4.756 | √ | √ | similar to N-acetylmuramoyl-L-alanine amidase (yomC) |
BS2803 | -4.750 | √ | √ | valyl-tRNA synthetase (valS) |
BS0093 | -4.747 | √ | √ | serine acetyltransferase (cysE) |
BS3877 | -4.696 | √ | hypothetical protein (yxkD) | |
BS1357 | -4.680 | √ | √ | hypothetical protein (ykrT) |
BS0178 | -4.675 | √ | L-glutamine-D-fructose-6-phosphate amidotransferase (glmS) | |
BS1658 | -4.644 | √ | DNA polymerase III (alpha subunit) (polC) | |
BS3894 | -4.630 | √ | hypothetical protein (yxjB) | |
tRNA-Arg | -4.609 | tRNA-Arg (trnJ-Arg) | ||
BS0535 | -4.505 | similar to antibiotic resistance protein (ydfB) | ||
BS3839 | -4.472 | √ | tyrosyl-tRNA synthetase (tyrZ) | |
BS2961 | -4.430 | √ | √ | tyrosyl-tRNA synthetase (tyrS) |
BS0441 | -4.399 | hypothetical protein (ydbB) | ||
BS1143 | -4.382 | √ | tryptophanyl-tRNA synthetase (trpS) | |
BS1737 | -4.375 | √ | similar to ribonucleoprotein (ymaA) | |
BS0254 | -4.309 | √ | √ | hypothetical protein (yczA) |
BS1971 | -4.297 | √ | similar to adenosylmethionine-8-amino-7-oxononanoate aminotransferase (yodT) | |
BS0643 | -4.279 | √ | √ | phosphoribosylaminoimidazole carboxylase I (purE) |
BS3026 | -4.270 | √ | √ | leucyl-tRNA synthetase (leuS) |
BS2889 | -4.249 | √ | threonyl-tRNA synthetase (thrS) | |
BS3690 | -4.191 | √ | hypothetical protein (ywlC) | |
BS1188 | -4.176 | √ | √ | similar to cystathionine gamma-synthase (yjcI) |
BS0521 | -4.158 | √ | hypothetical protein (ydeI) | |
BS2452 | -4.143 | √ | similar to aminomethyltransferase (yqhI) | |
BS3604 | -4.128 | √ | hypothetical protein (ywrE) | |
BS1313 | -4.086 | √ | gamma-glutamyl kinase (proB) | |
BS3269 | -3.989 | √ | √ | similar to ABC transporter (ATP-binding protein) (yusC) |
BS0423 | -3.974 | √ | hypothetical protein (ydaH) | |
BS2504 | -3.896 | √ | similar to transcriptional regulator (Fur family) (yqfV) | |
BS3900 | -3.884 | √ | √ | endo-beta-1,3-1,4 glucanase (bglS) |
BS0038 | -3.883 | √ | √ | methionyl-tRNA synthetase (metS) |
BS2319 | -3.879 | √ | hypothetical protein (ypuF) | |
BS1683 | -3.845 | similar to phage-related protein (ymfE) | ||
BS1881 | -3.805 | √ | phosphoenolpyruvate synthase (pps) | |
BS3513 | -3.805 | √ | putative membrane protein (csbA) | |
BS0432 | -3.796 | hypothetical protein (ydaO) | ||
BS3355 | -3.795 | hypothetical protein (yvaI) | ||
BS2858 | -3.784 | √ | √ | phenylalanyl-tRNA synthetase (alpha subunit) (pheS) |
BS3668 | -3.780 | √ | hypothetical protein (ywmD) | |
BS0927 | -3.776 | √ | glycerol uptake facilitator (glpF) | |
BS0281 | -3.739 | √ | hypothetical protein (ycdC) | |
BS2306 | -3.714 | RNA polymerase ECF-type sigma factor (sigma-X) (sigX) | ||
BS0143 | -3.709 | √ | RNA polymerase (alpha subunit) (rpoA) | |
BS0449 | -3.687 | √ | similar to ABC transporter (ATP-binding protein) (ydbJ) | |
BS1094 | -3.668 | √ | hypothetical protein (yitC) | |
BS1370 | -3.645 | √ | motility protein A (motA) | |
BS3785 | -3.618 | √ | hypothetical protein (ywdL) | |
BS0104 | -3.612 | √ | ribosomal protein L10 (BL5) (rplJ) | |
BS3313 | -3.584 | similar to iron-binding protein (yvrC) | ||
BS0716 | -3.572 | √ | hypothetical protein (yetH) | |
BS1889 | -3.524 | √ | response regulator aspartate phosphatase (rapK) | |
BS0673 | -3.492 | hypothetical protein (yerQ) | ||
BS0002 | -3.480 | DNA polymerase III (beta subunit) (dnaN) | ||
BS0880 | -3.473 | √ | transcriptional regulator (senS) | |
BS1548 | -3.473 | √ | √ | transcriptional attenuator and uracil phosphoribosyltransferase activity (minor) (pyrR) |
BS1409 | -3.467 | √ | hypothetical protein (ykuH) | |
BS2881 | -3.464 | initiation factor IF-3 (infC) | ||
BS1651 | -3.412 | uridylate kinase (smbA) | ||
BS3888 | -3.412 | √ | √ | hypothetical protein (yxjH) |
BS3889 | -3.412 | √ | √ | hypothetical protein (yxjG) |
BS0925 | -3.407 | √ | similar to adenosylmethionine-8-amino-7-oxononanoate aminotransferase (yhxA) | |
BS1205 | -3.351 | hypothetical protein (yjdG) | ||
BS3784 | -3.335 | hypothetical protein (spsA) | ||
BS3093 | -3.325 | √ | hypothetical protein (yuaJ) | |
BS1470 | -3.265 | √ | hypothetical protein (yktD) | |
BS1549 | -3.265 | √ | uracil permease (pyrP) | |
BS2841 | -3.262 | √ | aspartokinase II (lysC) | |
BS2903 | -3.222 | DNA polymerase I (polA) | ||
BS3446 | -3.202 | √ | hypothetical protein (yvdQ) | |
BS2984 | -3.202 | hypothetical protein (ytmQ) | ||
BS1920 | -3.201 | √ | similar to ATP-dependent DNA helicase (yocI) | |
BS3343 | -3.192 | √ | hypothetical protein (yvgV) | |
BS3731 | -3.192 | √ | hypothetical protein (ywiA) | |
BS3278 | -3.188 | similar to 3-hydroxyacyl-CoA dehydrogenase (yusL) | ||
BS3412 | -3.180 | transcriptional regulator (LacI family) (lacR) | ||
BS2278 | -3.156 | hypothetical protein (yphE) | ||
BS3914 | -3.141 | √ | hypothetical protein (yxiF) | |
BS1550 | -3.120 | √ | √ | aspartate carbamoyltransferase (pyrB) |
BS0878 | -3.120 | √ | thiamin biosynthesis protein (thiA) | |
BS2775 | -3.111 | √ | similar to sodium/proton-dependent alanine carrier protein (yrbD) | |
BS1673 | -3.111 | dipicolinate synthase subunit A (spoVFA) | ||
BS2569 | -3.086 | √ | site-specific DNA recombinase (spoIVCA) | |
BS2713 | -3.075 | √ | similar to formate dehydrogenase (yrhG) | |
BS2539 | -3.075 | heat-shock protein (dnaJ) | ||
BS3719 | -3.068 | similar to cardiolipin synthetase (ywiE) | ||
BS2711 | -3.061 | √ | similar to methyltransferase (yrhH) | |
BS1166 | -3.059 | √ | transcriptional regulator (tenA) | |
BS1446 | -3.057 | aminopeptidase (ampS) | ||
BS0503 | -3.033 | √ | hypothetical protein (yddM) | |
BS1455 | -3.014 | √ | hypothetical protein (ykzG) | |
BS3164 | -2.969 | √ | transcriptional regulator (comQ) | |
BS1360 | -2.966 | √ | √ | similar to ribulose-bisphosphate carboxylase (ykrW) |
BS1536 | -2.942 | √ | similar to acetylornithine deacetylase (ylmB) | |
BS3133 | -2.940 | √ | similar to polyribonucleotide nucleotidyltransferase (yugI) | |
BS3635 | -2.930 | √ | flagellar basal-body rod protein (flhO) | |
BS1659 | -2.908 | √ | hypothetical protein (ylxS) | |
BS2216 | -2.896 | hypothetical protein (ypsA) | ||
BS0115 | -2.894 | √ | ribosomal protein S10 (BS13) (rpsJ) | |
BS0637 | -2.878 | √ | hypothetical protein (yebB) | |
BS2627 | -2.867 | similar to transcriptional regulator (phage-related) (Xre family) (yqaE) | ||
BS0745 | -2.856 | √ | similar to quinone oxidoreductase (yfmJ) | |
BS1785 | -2.852 | transcriptional regulator (lexA) | ||
BS1737 | -2.805 | √ | similar to ribonucleoprotein (ymaA) | |
BS1525 | -2.800 | √ | cell-division initiation protein (divIB) | |
BS2138 | -2.782 | hypothetical protein (yomD) | ||
BS2162 | -2.776 | √ | hypothetical protein (yokC) | |
BS1335 | -2.740 | √ | similar to transcriptional regulator (MarR family) (ykoM) | |
BS0241 | -2.658 | √ | similar to histidine permease (ybgF) | |
BS2715 | -2.649 | √ | similar to formate dehydrogenase (yrhE) | |
BS1855 | -2.649 | √ | √ | similar to phosphoglycerate dehydrogenase (yoaD) |
BS2986 | -2.643 | √ | hypothetical protein (ytmP) | |
BS1321 | -2.642 | hypothetical protein (ispU) | ||
BS0386 | -2.640 | √ | similar to transcriptional regulator (TetR/AcrR family) (ycnC) | |
BS2425 | -2.616 | similar to exodeoxyribonuclease VII (large subunit) (yqiB) | ||
BS0057 | -2.589 | similar to amino acid transporter (yabM) | ||
BS3957 | -2.586 | similar to ABC transporter (ATP-binding protein) (yxdL) | ||
BS1003 | -2.585 | √ | Hit-like protein (hit) | |
BS3350 | -2.580 | hypothetical protein (yvaC) | ||
BS1659 | -2.573 | √ | hypothetical protein (ylxS) | |
BS4050 | -2.567 | √ | hypothetical protein (yybP) | |
BS2617 | -2.559 | √ | hypothetical protein (yqaN) | |
BS0806 | -2.555 | √ | acetoin dehydrogenase E1 component (TPP-dependent alpha subunit) (acoA) | |
BS0636 | -2.553 | √ | GMP synthetase (guaA) | |
BS1871 | -2.546 | √ | hypothetical protein (yoaS) | |
BS2152 | -2.537 | √ | hypothetical protein (yolA) | |
BS1490 | -2.535 | √ | cytochrome caa3 oxidase (subunit II) (ctaC) | |
BS3210 | -2.518 | transcriptional regulator (paiA) | ||
BS0558 | -2.516 | √ | hypothetical protein (ydgC) | |
BS1585 | -2.516 | similar to phosphoglycerate dehydrogenase (yloW) | ||
BS3625 | -2.513 | transcriptional regulator (DeoR family) (glcR) | ||
BS2512 | -2.483 | √ | hypothetical protein (yqfN) | |
BS0164 | -2.480 | similar to transcriptional regulator (AraC/XylS family) (ybbB) | ||
BS2895 | -2.471 | √ | hypothetical protein (ytcF) | |
BS2632 | -2.456 | √ | hypothetical protein (yrkS) | |
BS0804 | -2.447 | √ | hypothetical protein (yfjM) | |
BS0632 | -2.404 | √ | similar to cation efflux system membrane protein (yeaB) | |
BS2632 | -2.392 | √ | hypotheitcal protein (yrkS) | |
BS2713 | -2.387 | √ | similar to formate dehydrogenase (yrhG) | |
BS0561 | -2.386 | √ | ATP-binding transport protein (expZ) | |
BS1373 | -2.372 | √ | hypothetical protein (ykvJ) | |
BS0888 | -2.371 | √ | hypothetical protein (ygaO) | |
BS2239 | -2.369 | ketopantoate hydroxymethyltransferase (panB) | ||
BS2746 | -2.356 | √ | hypothetical protein (yrvN) | |
BS3568 | -2.347 | UDP-glucose:polyglycerol phosphate glucosyltransferase (tagE) | ||
BS4087 | -2.342 | √ | similar to formate dehydrogenase (yyaE) | |
BS0745 | -2.309 | √ | similar to quinone oxidoreductase (yfmJ) | |
BS3473 | -2.308 | √ | similar to mutator MutT protein (yvcI) | |
BS2596 | -2.308 | √ | similar to phage-related protein (yqbN) | |
BS1319 | -2.296 | √ | cobalamin-independent methionine synthase (metC) | |
BS1472 | -2.294 | √ | hypothetical protein (ylaA) | |
BS3265 | -2.287 | √ | similar to ABC transporter (ATP-binding protein) (yurY) | |
BS3666 | -2.250 | required for formate dehydrogenase activity (narQ) | ||
BS2225 | -2.236 | √ | hypothetical protein (yppD) | |
BS3000 | -2.232 | √ | hypothetical protein (ytfP) | |
BS1181 | -2.230 | √ | hypothetical protein (yjcB) | |
BS1735 | -2.220 | hypothetical protein (ymzC) | ||
BS0668 | -2.210 | √ | hypothetical protein (yerL) | |
BS1065 | -2.204 | similar to DNA exonuclease (yirY) | ||
BS3199 | -2.201 | √ | hypothetical protein (yuiF) | |
BS1302 | -2.182 | hypothetical protein (ykgB) | ||
BS2921 | -2.181 | hypothetical protein (ytoI) | ||
BS3142 | -2.171 | √ | similar to multidrug-efflux transporter (yuxJ) | |
BS2729 | -2.163 | √ | similar to caffeoyl-CoA O-methyltransferase (yrrM) | |
BS0313 | -2.157 | hypothetical protein (ycgI) | ||
BS3278 | -2.157 | similar to 3-hydroxyacyl-CoA dehydrogenase (yusL) | ||
BS1386 | -2.151 | √ | similar to heavy metal-transporting ATPase (ykvW) | |
BS0245 | -2.139 | √ | similar to two-component sensor histidine kinase [YcbB] (ycbA) | |
BS3196 | -2.124 | √ | hypothetical protein (yuiI) | |
BS0826 | -2.115 | √ | similar to metabolite transport protein (yfiG) | |
BS1536 | -2.115 | √ | similar to acetylornithine deacetylase (ylmB) | |
BS1142 | -2.104 | hypothetical protein (yjbA) | ||
BS2376 | -2.057 | √ | √ | similar to pyrroline-5-carboxylate reductase (yqjO) |
BS2920 | -2.018 | hypothetical protein (ytpI) | ||
BS1878 | -2.018 | beta-lactamase precursor (penP) |