Table 5 List of all orthologous genes in the six gram-positive bacteria genomes in which two or more genomes share predicted attenuators
From: Identification of attenuation and antitermination regulation in prokaryotes
B. subtilis | B. halodurans | L. innocua | S. aureus | C. acetobutylicum | L. lactis | S. pneumoniae | ||||||||
IDa | Z-scoreb | IDa | No. of predictionsc | IDa | No. of predictionsc | IDa | No. of predictionsc | IDa | No. of predictionsc | IDa | No. of predictionsc | IDa | No. of predictionsc | Gened |
BS1310 | -6.836 | BH0686 | 1 | lin0846 | 0 | - | - | - | - | - | - | - | - | chaperonin (ykkC) |
BS3710 | -5.196 | BH3792 | 1 | lin2704 | 1 | SAV2127 | 0 | CAC2892 | 0 | L88252 | 1 | SP0494 | 2 | CTP synthetase (ctrA) |
BS2484 | -5.148 | BH1417 | 0 | lin1373 | 1 | SAV1550 | 1 | CAC1090 | 0 | L172782 | 0 | SP2095 | 0 | 5-formyltetrahydrofolate cyclo-ligase |
(yqgN) | ||||||||||||||
BS0183 | -4.938 | - | - | - | - | SAV0452 | 1 | - | - | - | - | - | - | NADH dehydrogenase (subunit 5) |
(ndhF) | ||||||||||||||
BS3877 | -4.696 | - | - | lin1219 | 1 | SAV0646 | 0 | - | - | - | - | - | - | hypothetical protein (yxkD) |
BS0535 | -4.505 | BH2084 | 1 | - | - | - | - | - | - | - | - | - | - | antibiotic resistance protein (ydfB) |
BS2452 | -4.143 | BH2816 | 0 | lin1385 | 0 | SAV1537 | 1 | - | - | - | - | - | - | aminomethyltransferase (yqhI) |
BS0143 | -3.709 | BH0162 | 1 | lin2755 | 0 | SAV2224 | 0 | CAC3104 | 0 | L0136 | 0 | SP0236 | 0 | RNA polymerase (alpha subunit) |
(rpoA) | ||||||||||||||
BS0104 | -3.612 | BH0121 | 1 | lin0282 | 1 | SAV0539 | 0 | CAC3146 | 0 | L0407 | 0 | SP1355 | 0 | ribosomal protein L10 (rplJ) |
BS0002 | -3.480 | BH0002 | 0 | lin0002 | 0 | SAV0002 | 0 | CAC0002 | 1 | L0275 | 0 | SP0002 | 0 | DNA polymerase III (beta subunit) |
(dnaN) | ||||||||||||||
BS2881 | -3.464 | BH3140 | 1 | lin1897 | 1 | SAV1680 | 1 | CAC2361 | 1 | L95240 | 1 | SP0959 | 0 | initiation factor IF-3 (infC) |
BS3093 | -3.325 | BH0830 | 0 | lin1468 | 1 | - | - | CAC2928 | 1 | L116212 | 0 | - | - | hypothetical protein (yuaJ) |
BS2841 | -3.262 | BH3096 | 1 | lin1198 | 0 | SAV1393 | 1 | - | - | - | - | - | - | aspartokinase II (lysC) |
BS2903 | -3.222 | BH3153 | 0 | lin1600 | 1 | SAV1690 | 1 | CAC1098 | 2 | L0270 | 0 | SP0032 | 0 | DNA polymerase I (polA) |
BS1920 | -3.201 | - | - | lin2900 | 0 | SAV0721 | 0 | CAC2687 | 1 | L0268 | 0 | - | - | ATP-dependent DNA helicase (yocI) |
BS3731 | -3.192 | - | - | - | - | - | - | CAC2795 | 0 | L19128 | 1 | - | - | hypothetical protein (ywiA) |
BS2278 | -3.156 | BH1643 | 1 | - | - | - | - | - | - | - | - | - | - | hypothetical protein (yphE) |
BS0878 | -3.120 | BH1933 | 1 | - | - | - | - | CAC3014 | 1 | - | - | - | - | thiamin biosynthesis protein (thiA) |
BS2539 | -3.075 | BH1348 | 0 | lin1509 | 0 | SAV1579 | 1 | CAC1283 | 1 | L0272 | 1 | SP0519 | 0 | heat-shock protein (dnaJ) |
BS1659 | -2.908 | BH2417 | 0 | lin1358 | 1 | SAV1265 | 0 | CAC1798 | 1 | L173151 | 1 | SP0552 | 0 | hypothetical protein (ylxS) |
BS0115 | -2.894 | BH0133 | 1 | lin2782 | 0 | SAV2251 | 1 | CAC3134 | 0 | L0387 | 1 | SP0208 | 0 | ribosomal protein S10 (rpsJ) |
BS0637 | -2.878 | BH0608 | 1 | lin0582 | 0 | SAV2253 | 0 | CAC2772 | 0 | - | - | - | - | hypothetical protein (yebB) |
BS2627 | -2.867 | - | - | lin0073 | 0 | SAV1098 | 1 | - | - | - | - | - | - | transcriptional regulator (yqaE) |
BS2986 | -2.643 | BH3263 | 0 | lin1657 | 0 | SAV1749 | 1 | - | - | L155396 | 0 | SP0549 | 0 | hypothetical protein (ytmP) |
BS1659 | -2.573 | BH2417 | 0 | lin1358 | 1 | SAV1265 | 0 | CAC1798 | 1 | L173151 | 1 | SP0552 | 0 | hypothetical protein (ylxS) |
BS0636 | -2.553 | BH0607 | 1 | lin1081 | 0 | SAV0391 | 0 | CAC2700 | 0 | L115968 | 1 | SP1445 | 0 | GMP synthetase (guaA) |
BS0558 | -2.516 | - | - | lin1827 | 1 | - | - | - | - | L53789 | 1 | - | - | hypothetical protein (ydgC) |
BS2512 | -2.483 | BH1379 | 0 | lin1490 | 0 | SAV1560 | 1 | CAC1302 | 0 | L84257 | 0 | SP1610 | 0 | hypothetical protein (yqfN) |
BS0561 | -2.386 | - | - | - | - | - | - | CAC3007 | 2 | - | - | - | - | ATP-binding transport protein (expZ) |
BS3473 | -2.308 | BH3570 | 0 | lin1215 | 1 | SAV0467 | 0 | CAC0084 | 0 | L0288 | 0 | SP0740 | 0 | mutator protein (yvcI) |
BS1319 | -2.296 | BH0438 | 1 | lin1789 | 1 | SAV0356 | 0 | - | - | L0100 | 0 | SP0585 | 0 | cobalamin-independent methionine |
synthase (metC) | ||||||||||||||
BS3265 | -2.287 | BH3471 | 0 | lin2510 | 0 | SAV0842 | 0 | CAC3288 | 1 | L34806 | 0 | SP0867 | 1 | ABC transporter (ATP-binding |
protein) (yurY) | ||||||||||||||
BS0668 | -2.210 | BH0665 | 0 | lin1868 | 0 | SAV1901 | 0 | CAC2671 | 1 | L0475 | 0 | SP0438 | 0 | glutamyl-tRNA(Gln) |
amidotransferase (subunit C) (yerL) | ||||||||||||||
BS2729 | -2.163 | BH1272 | 0 | lin1533 | 0 | SAV1614 | 1 | CAC1686 | 0 | L165684 | 0 | SP0980 | 0 | O-methyltransferase (yrrM) |
BS1386 | -2.151 | BH0744 | 0 | lin0644 | 1 | - | - | - | - | L63697 | 0 | - | - | heavy metal-transporting ATPase |
(ykvW) | ||||||||||||||
BS0019 | - | BH0034 | 1 | lin2852 | 0 | SAV0478 | 0 | CAC0125 | 1 | L0279 | 0 | SP0865 | 0 | DNA polymerase III (gamma and tau |
subunits) (dnaX) | ||||||||||||||
BS0106 | - | BH0124 | 1 | lin0284 | 0 | SAV0541 | 0 | CAC0877 | 0 | L65498 | 0 | SP0841 | 1 | hypothetical protein (ybxB) |
BS0107 | - | BH0126 | 0 | lin0285 | 1 | SAV0542 | 1 | CAC3143 | 1 | L0137 | 1 | SP1961 | 1 | DNA-directed RNA polymerase (beta |
subunit) (rpoB) | ||||||||||||||
BS0112 | - | BH0131 | 0 | lin2803 | 0 | SAV0547 | 0 | CAC3138 | 1 | L0368 | 1 | SP0273 | 0 | elongation factor G (fus) |
BS0462 | - | BH0518 | 0 | lin0884 | 0 | SAV2071 | 0 | CAC0489 | 1 | L61355 | 1 | SP1699 | 0 | acyl carrier protein synthase (ydcB) |
BS0516 | - | BH0725 | 0 | - | - | SAV2534 | 1 | CAC0875 | 1 | L124727 | 0 | SP1447 | 0 | hypothetical protein (ydeD) |
BS0663 | - | BH0649 | 0 | lin1870 | 0 | SAV1904 | 0 | CAC2673 | 0 | L0304 | 1 | SP1117 | 1 | DNA ligase (yerG) |
BS0692 | - | - | - | lin0655 | 0 | SAV1419 | 0 | CAC2751 | 1 | L36177 | 1 | SP1464 | 0 | hypothetical protein (yesJ) |
BS0824 | - | BH3305 | 0 | lin0649 | 1 | SAV2522 | 0 | - | - | - | - | SP0073 | 1 | hypothetical protein (yfiE) |
BS0892 | - | BH1023 | 0 | - | - | SAV1855 | 0 | CAC0700 | 0 | L161988 | 1 | SP0486 | 1 | rRNA methylase (cspR) |
BS0960 | - | BH2987 | 1 | - | - | SAV1783 | 0 | CAC1586 | 1 | - | - | SP1295 | 0 | hypothetical protein (yhdV) |
BS0988 | - | BH0202 | 0 | lin1781 | 0 | SAV1045 | 0 | CAC2712 | 1 | L0171 | 1 | SP0415 | 1 | similar to 3-hydroxybutyryl-CoA |
dehydratase (yhaR) | ||||||||||||||
BS1062 | - | - | - | lin2369 | 0 | SAV0966 | 0 | CAC2263 | 1 | L0252 | 1 | SP1151 | 0 | ATP-dependent deoxyribonuclease |
(subunit B) (addB) | ||||||||||||||
BS1139 | - | BH3636 | 0 | lin0182 | 1 | SAV0991 | 0 | CAC3179 | 1 | L88446 | 0 | - | - | oligopeptide ABC transporter |
(oligopeptide-binding protein) (appA) | ||||||||||||||
BS1269 | - | BH0012 | 1 | lin2568 | 0 | SAV1955 | 1 | CAC1883 | 0 | L60836 | 0 | - | - | prophage (xkd0) |
BS1345 | - | BH2553 | 1 | lin0990 | 1 | SAV1022 | 1 | CAC1415 | 0 | - | - | - | - | similar to toxic anion resistance |
protein (ykoY) | ||||||||||||||
BS1390 | - | BH0844 | 1 | - | - | SAV0189 | 1 | CAC0570 | 0 | - | - | SP1684 | 0 | PTS glucose-specific enzyme II ABC |
component (ptsG) | ||||||||||||||
BS1478 | - | BH2632 | 0 | lin1055 | 1 | SAV1109 | 0 | CAC1684 | 0 | L0370 | 1 | SP0681 | 0 | similar to GTP-binding elongation |
factor (ylaG) | ||||||||||||||
BS1512 | - | BH2579 | 0 | lin2152 | 1 | SAV2443 | 2 | CAC2937 | 0 | L157055 | 1 | - | - | similar to ketopantoate reductase |
(ylbQ) | ||||||||||||||
BS1514 | - | BH2576 | 1 | lin2148 | 1 | SAV1178 | 0 | CAC2133 | 0 | - | - | - | - | hypothetical protein (yllB) |
BS1553 | - | BH2536 | 0 | lin1949 | 0 | SAV1203 | 0 | CAC2644 | 0 | L198033 | 2 | SP1275 | 1 | carbamoyl-phosphate synthase |
(catalytic subunit) (pyrAB) | ||||||||||||||
BS1566 | - | BH2515 | 1 | lin0832 | 0 | - | - | CAC2137 | 0 | L2866 | 1 | SP1551 | 1 | cation-transporting ATPase (yloB) |
BS1570 | - | BH2510 | 0 | lin1939 | 1 | SAV1211 | 1 | CAC1720 | 0 | L166912 | 0 | SP1231 | 0 | pantothenate metabolism flavoprotein |
(yloI) | ||||||||||||||
BS1587 | - | BH2495 | 0 | lin1925 | 0 | SAV1227 | 0 | CAC1736 | 1 | L0262 | 1 | SP1697 | 0 | ATP-dependent DNA helicase recG |
(ylpB) | ||||||||||||||
BS1614 | - | BH1529 | 0 | lin1316 | 0 | SAV1252 | 0 | CAC2066 | 0 | L34517 | 1 | SP0890 | 1 | integrase/recombinase (codV) |
BS1650 | - | BH2426 | 0 | lin1766 | 0 | SAV1257 | 1 | CAC1788 | 0 | L0376 | 1 | SP2214 | 0 | elongation factor Ts (tsf) |
BS1653 | - | BH2423 | 1 | lin1352 | 1 | SAV1260 | 1 | CAC1791 | 0 | L183602 | 0 | SP0261 | 1 | undecaprenyl diphosphate synthetase |
(yluA) | ||||||||||||||
BS1668 | - | BH2408 | 0 | lin1367 | 1 | SAV1273 | 0 | CAC1807 | 1 | L0392 | 0 | SP1626 | 0 | ribosomal protein S15 (rpsO) |
BS1669 | - | BH2407 | 0 | lin1368 | 1 | SAV1274 | 1 | CAC1808 | 0 | L0325 | 0 | SP0588 | 1 | polyribonucleotide phosphorylase |
(pnpA) | ||||||||||||||
BS1677 | - | BH1742 | 1 | lin1474 | 0 | SAV1395 | 0 | CAC2378 | 0 | L0093 | 1 | SP1014 | 0 | dihydrodipicolinate synthase (dapA) |
BS2023 | - | BH3508 | 0 | - | - | - | - | CAC1501 | 1 | - | - | SP1336 | 1 | DNA-methyltransferase (Bsu) (mtbP) |
BS2185 | - | BH3062 | 0 | lin2090 | 1 | SAV2053 | 1 | CAC3170 | 0 | L0077 | 0 | SP2126 | 1 | dihydroxy-acid dehydratase (ilvD) |
BS2258 | - | BH1665 | 0 | lin2039 | 0 | SAV0724 | 1 | CAC3031 | 1 | L0065 | 0 | - | - | histidinol-phosphate aminotransferase |
(hisC) | ||||||||||||||
BS2264 | - | BH1659 | 1 | lin1674 | 1 | SAV1367 | 1 | CAC3163 | 1 | L0054 | 1 | SP1817 | 1 | anthranilate synthase (trpE) |
BS2301 | - | - | - | lin2059 | 1 | SAV1485 | 0 | CAC2841 | 1 | L106755 | 0 | SP0488 | 0 | hypothetical protein (ypaA) |
BS2324 | - | BH1554 | 1 | - | - | SAV1771 | 1 | CAC0590 | 0 | L0163 | 2 | SP0178 | 2 | riboflavin-specific deaminase (ribG) |
BS2334 | - | BH1544 | 1 | lin2066 | 0 | SAV1400 | 0 | CAC0608 | 1 | L0121 | 0 | SP1978 | 0 | diaminopimelate decarboxylase (lysA) |
BS2383 | - | BH1472 | 0 | lin2082 | 0 | SAV1895 | 1 | CAC0285 | 0 | L0305 | 0 | SP0458 | 1 | DNA-damage inducible protein |
(yqjH) | ||||||||||||||
BS2661 | - | - | - | - | - | SAV1407 | 0 | CAC1610 | 1 | - | - | SP0626 | 1 | branched-chain amino acid |
transporter (brnQ) | ||||||||||||||
BS2741 | - | BH1262 | 1 | lin1545 | 0 | SAV1620 | 1 | CAC1067 | 0 | - | - | - | - | hypothetical protein (yrrB) |
BS2747 | - | BH1255 | 1 | - | - | SAV1628 | 1 | CAC0908 | 0 | - | - | SP0695 | 0 | hypothetical protein (yrvM) |
BS2932 | - | BH0170 | 0 | lin2443 | 0 | SAV2414 | 0 | CAC3325 | 1 | L162009 | 1 | SP0148 | 0 | similar to amino acid ABC |
transporter (binding protein) (ytmJ) | ||||||||||||||
BS2942 | - | BH3193 | 0 | lin1617 | 0 | SAV1712 | 1 | - | - | L74738 | 1 | SP2045 | 1 | hypothetical protein (ytxK) |
BS3015 | - | BH0783 | 1 | - | - | SAV2427 | 1 | CAC1361 | 0 | - | - | - | - | dethiobiotin synthetase (bioD) |
BS3049 | - | BH3300 | 1 | lin1773 | 1 | SAV1790 | 1 | CAC2856 | 1 | L153408 | 1 | SP0762 | 0 | S-adenosylmethionine synthetase |
(metK) | ||||||||||||||
BS3345 | - | BH0557 | 0 | lin1967 | 0 | SAV2557 | 1 | CAC3655 | 0 | L45966 | 1 | SP0729 | 0 | heavy metal-transporting ATPase |
(yvgX) | ||||||||||||||
BS3388 | - | BH3559 | 0 | lin2552 | 1 | SAV0773 | 1 | CAC0710 | 1 | L0010 | 0 | SP0499 | 0 | 3-phosphoglycerate kinase (pgk) |
BS3496 | - | BH0421 | 0 | lin0955 | 1 | SAV0701 | 1 | CAC0188 | 0 | L173068 | 0 | SP2056 | 0 | N-acetylglucosamine-6-phosphate |
deacetylase (nagA) | ||||||||||||||
BS3705 | - | BH3784 | 0 | lin2697 | 0 | SAV2124 | 0 | CAC3539 | 1 | L113067 | 1 | SP1081 | 0 | UDP-N-acetylglucosamine 1- |
carboxyvinyltransferase (murZ) | ||||||||||||||
BS3728 | - | BH0834 | 1 | lin2706 | 0 | SAV0607 | 0 | CAC1041 | 1 | L0344 | 0 | SP2078 | 0 | arginyl-tRNA synthetase (argS) |
BS3729 | - | BH3809 | 1 | lin2707 | 0 | SAV0606 | 1 | CAC2894 | 0 | - | - | - | - | hypothetical protein (ywiB) |
BS3875 | - | BH1141 | 0 | lin2875 | 1 | - | - | CAC3236 | 0 | L26721 | 1 | SP0593 | 0 | hypothetical protein (yxkF) |
BS3901 | - | BH0297 | 0 | lin2530 | 1 | SAV1357 | 0 | CAC0422 | 1 | L0154 | 1 | SP0576 | 0 | transcriptional antiterminator (BglG |
family) (licT) | ||||||||||||||
BS3916 | - | - | - | lin0454 | 1 | - | - | CAC1057 | 1 | - | - | - | - | cell wall-associated protein precursor |
(wapA) | ||||||||||||||
BS3918 | - | BH3184 | 1 | lin1615 | 0 | SAV1710 | 0 | - | - | L84477 | 1 | SP1996 | 0 | hypothetical protein (yxiE) |
BS3919 | - | - | - | lin0344 | 1 | - | - | CAC0743 | 1 | - | - | SP0578 | 0 | beta-glucosidase (bglH) |
BS4099 | - | BH4065 | 0 | lin2987 | 0 | SAV2713 | 1 | CAC3738 | 1 | L131443 | 0 | SP2042 | 0 | ribonuclease P (protein component) |
(rnpA) | ||||||||||||||
- | - | BH0440 | 2 | - | - | SAV0142 | 1 | - | - | L97415 | 0 | - | - | phosphonate ABC transporter ATP- |
binding protein | ||||||||||||||
- | - | BH0503 | 0 | - | - | - | - | CAC2487 | 1 | L3279 | 0 | SP0204 | 1 | hypothetical protein |
- | - | BH0595 | 1 | lin0026 | 1 | - | - | CAC1407 | 1 | L90678 | 0 | - | - | PTS beta-glucoside-specific enzyme |
II ABC component | ||||||||||||||
- | - | BH2025 | 1 | lin2903 | 1 | - | - | - | - | - | - | - | - | ABC transporter (ATP-binding |
protein) | ||||||||||||||
- | - | BH2200 | 1 | - | - | - | - | - | - | L0358 | 1 | SP2229 | 0 | tryptophanyl-tRNA synthetase |
- | - | BH2603 | 0 | lin0604 | 1 | - | - | CAC2783 | 1 | L75975 | 0 | - | - | O-acetylhomoserine sulfhydrylase |
- | - | - | - | - | - | - | - | CAC1072 | 1 | L180742 | 1 | - | - | hypothetical protein |
- | - | - | - | - | - | - | - | - | - | L49741 | 1 | SP1647 | 1 | endopeptidase |
- | - | - | - | - | - | - | - | - | - | L90622 | 1 | SP0861 | 1 | hypothetical protein |
- | - | - | - | lin1136 | 1 | - | - | CAC2721 | 1 | - | - | - | - | similar to two-component response |
regulator | ||||||||||||||
- | - | - | - | lin1443 | 1 | SAV0226 | 0 | CAC0980 | 1 | L57408 | 0 | SP0459 | 0 | pyruvate-formate lyase |
- | - | - | - | lin1851 | 1 | - | - | CAC3619 | 0 | - | - | SP1502 | 1 | similar to amino acid (glutamine) |
ABC transporter, permease protein | ||||||||||||||
- | - | - | - | lin2124 | 1 | SAV1402 | 1 | CAC2990 | 0 | - | - | - | - | major cold-shock protein |