|
Predicted attenuators in the genome of B. subtilis |
||||
| 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) |
||
|
First column is gene ID, second is Z score based on method in Materials and methods. Third column is checked if an attenuator has already been shown experimentally. Fourth column indicates if a promoter was predicted from NNPP program. Fifth column lists gene description. a. The NNPP program (cutoff = 0.8) was used for the upstream promoter prediction b GenBank annotation was used for gene definitions and gene names | ||||
Lathe et al. Genome Biology 2002 3:preprint0003.1 doi:10.1186/gb-2002-3-6-preprint0003 |
||||