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Table 30 Top entropy hits in E. coli

From: Secondary structural entropy in RNA switch (Riboswitch) identification

E. coli Start End Strand Upstream operon Dist. to upstream MFE MFE p. Val. GC RND RND p. Val. Uracil Dist. to downstream Downstream operon Probability
100 nt 4083889 4083988 forward yiiF -5848 -38.4 0.0267 0.53 58.6367989 0.0365 0.29 102 fdhD 0.789
100 nt 187962 188061 forward cdaR -4293 -36.4 0.0466 0.53 59.0985985 0.0229 0.32 1702 rpsB,tff,tsf 0.776
100 nt 952485 952584 forward ycaK -2955 -36.8 0.0419 0.52 58.3203011 0.0494 0.27 3452 ycaP 0.765
100 nt 4115038 4115137 forward uspD,yiiS -3245 -37 0.0396 0.53 58.3563995 0.0477 0.33 1452 zapB 0.756
E. coli Start End Strand Upstream operon Dist. to upstream MFE MFE p. Val. GC RND RND p. Val. Uracil Dist. to downstream Downstream operon Probability
150 nt 2686923 2687072 forward hmp -1797 -56.00 - 0.5333 90.7522964 0.0077 0.32000 6822 mltF 0.8671584129
150 nt 452721 452870 forward yajQ -8244 -60.90 - 0.5200 88.2920990 - 0.23333 897 bolA 0.8664909005
150 nt 1100699 1100848 forward ycdZ -610 -58.70 - 0.4933 87.8781967 - 0.30666 2397 csgA,csgB,csgC 0.8559710383
150 nt 2887386 2887535 forward iap -11667 -56.40 - 0.5333 89.1240005 0.0294 0.31333 2772 queD 0.8254097700
150 nt 3467187 3467336 forward gspO1 -2866 -56.10 - 0.5200 88.5419006 0.0450 0.29333 8397 slyX 0.8172816634
150 nt 2553118 2553267 forward amiA,hemF -893 -57.40 - 0.5133 87.6467972 - 0.28666 3597 intZ 0.8125300407
150 nt 2660264 2660413 forward ryfA -8005 -56.90 - 0.5000 87.1239014 - 0.32000 1122 suhB 0.8031908870
150 nt 1766798 1766947 forward lpp -11038 -57.00 - 0.4800 85.6548004 - 0.25333 222 ydiK 0.7757616639
150 nt 1718374 1718523 forward slyB 72 -58.70 - 0.4867 85.1240005 - 0.32666 597 ydhI,ydhJ,ydhK 0.7731205821
150 nt 4356712 4356861 forward yjdK,yjdO -5529 -58.80 - 0.5200 86.0333023 - 0.26000 9897 fxsA 0.7661048174
150 nt 149580 149729 forward yadD -1631 -57.80 - 0.4600 84.3807983 - 0.30666 12447 hrpB 0.7651519775
150 nt 4604476 4604625 forward yjjZ -334 -57.20 - 0.4867 85.4507980 - 0.27333 1272 holD,rimI,yjjG 0.7621335387
150 nt 3120069 3120218 forward C0719 -389 -56.40 - 0.5267 87.1032028 - 0.27333 6147 glcC 0.7610746622
150 nt 1982024 1982173 forward uspC -3740 -56.20 - 0.5333 87.3750000 - 0.26666 2847 ftnB 0.7596676350
150 nt 3921878 3922027 forward cbrB,cbrC -25167 -56.00 - 0.4933 85.5883026 - 0.30666 3222 asnA 0.7384917736
150 nt 790921 791070 forward aroG -4934 -57.00 - 0.5333 86.4469986 - 0.28000 2997 acrZ 0.7345629930
150 nt 4482291 4482440 forward yjgN -3263 -58.30 - 0.5200 85.4577026 - 0.28666 1872 lptF,lptG 0.7340587974
150 nt 518357 518506 forward ybbL,ybbM -1692 -57.10 - 0.5000 85.1729965 - 0.26000 522 ybbA,ybbP 0.7300664783
150 nt 1167546 1167695 forward ycfJ -106 -57.70 - 0.5333 85.9982986 - 0.27333 672 bhsA 0.7274026275
150 nt 1642496 1642645 forward cspF -2326 -56.00 - 0.5333 86.4957962 - 0.25333 1347 ydfV 0.7190257311
150 nt 3916103 3916252 forward cbrB,cbrC -19392 -60.90 - 0.5200 84.0416031 - 0.30000 8997 asnA 0.7181233764
150 nt 3258127 3258276 forward yhaK,yhaL -4819 -55.70 - 0.5267 86.1580963 - 0.26000 7197 tdcR 0.7085512877
150 nt 3721360 3721509 forward insK -1209 -57.70 - 0.5133 84.8648987 - 0.26000 2472 wecH 0.7070741653
150 nt 2438211 2438360 forward flk -1165 -58.50 - 0.5267 84.9561996 - 0.24000 1497 mnmC 0.7053987384
150 nt 1268246 1268395 forward kdsA,ychA,ychQ 75 -56.90 - 0.4933 84.3839035 - 0.29333 222 rdlA 0.7012539506
150 nt 219458 219607 forward arfB,nlpE,yaeQ -3400 -59.90 - 0.5267 84.2009964 - 0.27333 3297 gmhB 0.6966923475
150 nt 3514668 3514817 forward frlA,frlB,frlC,frlD,frlR -11784 -56.50 - 0.5333 85.6490021 - 0.27333 6147 mrcA 0.6895118356
150 nt 3313884 3314033 forward psrO -4385 -55.60 - 0.5067 84.9284973 - 0.28666 2697 argG 0.6809250712
150 nt 649808 649957 forward ybdR -7180 -58.10 - 0.5333 84.6990967 - 0.25333 1572 dpiA,dpiB 0.6750817299
150 nt 2243989 2244138 forward yeiG -1142 -57.10 - 0.5333 84.3582993 - 0.26000 3672 yeiH 0.6381362677
150 nt 4253685 4253834 forward ubiA,ubiC -1695 -55.80 - 0.5267 84.4711990 - 0.29333 897 dgkA 0.6285824776
150 nt 2866503 2866652 forward ygbN -1937 -56.80 - 0.5333 84.2586975 - 0.30000 8022 iap 0.6268372536
150 nt 3576825 3576974 reverse yhhW -69 -55.60 - 0.4800 88.6371994 0.0419 0.30666 154 gntK,gntR,gntU 0.8547886610
150 nt 260750 260899 reverse yafW,yafX,yafY,ykfB,ykfF,ykfG,ykfH,ykfI -1723 -62.00 - 0.5267 86.8554001 - 0.32000 1504 phoE 0.8323625326
150 nt 2195866 2196015 reverse yehS -13803 -58.00 - 0.5333 88.6897964 0.0405 0.27333 3754 mrp 0.8320623040
150 nt 4176725 4176874 reverse sroH -11546 -58.80 - 0.5333 88.1481018 - 0.28000 3754 coaA 0.8252514601
150 nt 133211 133360 reverse speD,speE,yacC -1498 -56.40 - 0.5133 88.0559998 - 0.28000 2029 yacH 0.8126859665
150 nt 44332 44481 reverse apaG,apaH,lptD,pdxA,rsmA,surA -5969 -64.00 - 0.5333 85.3160019 - 0.26000 2479 caiA,caiB,caiC,caiD,caiE,caiT 0.8009238243
150 nt 2248916 2249065 reverse nupX -1922 -55.70 - 0.5333 88.3962021 - 0.28000 1354 yeiE 0.7910096645
150 nt 2774331 2774480 reverse ypjA -1758 -55.60 - 0.5200 87.4978027 - 0.26666 3229 ypjM_1,ypjM_2 0.7727379203
150 nt 2184269 2184418 reverse yehA,yehB,yehC,yehD -1054 -56.20 - 0.5333 87.6942978 - 0.30666 529 rcnR 0.7722578049
150 nt 1655707 1655856 reverse mlc,ynfK -8762 -58.20 - 0.5267 86.6440964 - 0.24000 304 ynfC 0.7716723680
150 nt 2168389 2168538 reverse gatR_2 -951 -56.70 - 0.5133 86.7958984 - 0.31333 304 gatR_1 0.7715415359
150 nt 3481959 3482108 reverse yhfA -1398 -57.90 - 0.5333 86.7799988 - 0.25333 2854 kefB,kefG,yheV 0.7633723617
150 nt 314642 314791 reverse ykgA -953 -58.20 - 0.5067 85.1943970 - 0.32000 2254 ykgR 0.7403761148
150 nt 2783559 2783708 reverse ileY -146 -56.20 - 0.4667 84.4744034 - 0.26666 604 ypjC 0.7329583764
150 nt 4050403 4050552 reverse glnA,glnG,glnL -1410 -56.70 - 0.5267 86.2409973 - 0.27333 1729 yihA 0.7301918864
150 nt 2465055 2465204 reverse yfdK,yfdL,yfdM,yfdN,yfdO -3965 -58.50 - 0.5333 85.6035004 - 0.25333 2104 mlaA 0.7242872119
150 nt 2809717 2809866 reverse luxS -2444 -56.20 - 0.5333 86.4486008 - 0.29333 11779 ygaC 0.7205215693
150 nt 3341463 3341612 reverse elbB,mtgA -5561 -57.50 - 0.5000 84.6742020 - 0.28000 3454 mlaB,mlaC,mlaD,mlaE,mlaF 0.7152099609
150 nt 1950122 1950271 reverse torY,torZ -2401 -56.44 - 0.5200 85.7341003 - 0.24666 1654 aspS 0.7131192684
150 nt 3059434 3059583 reverse ygfI -4786 -56.20 - 0.4933 84.9087982 - 0.27333 1879 yqfE 0.7122740149
150 nt 2530006 2530155 reverse pdxK -4323 -58.20 - 0.5000 84.2724991 - 0.25333 829 zipA 0.7098694444
150 nt 757742 757891 reverse mngR -6555 -57.90 - 0.4867 83.9291000 - 0.31333 4129 gltA 0.7092900276
150 nt 4452551 4452700 reverse fbp -4 -56.90 - 0.5200 85.3691025 - 0.29333 4954 ppa 0.7049999237
150 nt 3584997 3585146 reverse ugpA,ugpB,ugpC,ugpE,ugpQ -317 -59.30 - 0.5133 84.1650009 - 0.32000 229 ggt 0.7046704292
150 nt 3459796 3459945 reverse bfd,bfr -4396 -59.60 - 0.5200 84.1896973 - 0.23333 6454 gspA,gspB 0.7009978294
150 nt 3395856 3396005 reverse mreB,mreC,mreD -474 -56.20 - 0.5000 84.8627014 - 0.25333 1654 yhdP 0.6998521686
150 nt 2321601 2321750 reverse yfaA,yfaP,yfaQ,yfaS_1,yfaS_2,yfaT -3709 -61.10 - 0.5333 83.9000015 - 0.24000 3829 rcsC 0.6947578788
150 nt 4169919 4170068 reverse coaA -2101 -56.20 - 0.4933 84.4697037 - 0.26000 8704 trmA 0.6920779943
150 nt 4029970 4030119 reverse mobA,mobB -8880 -57.80 - 0.5133 84.4968033 - 0.30000 1054 fadA,fadB 0.6919249892
150 nt 2366493 2366642 reverse pmrD -4722 -56.00 - 0.5200 85.1843033 - 0.28000 2929 ais 0.6792802215
150 nt 1850076 1850225 reverse ydjE -490 -57.40 - 0.5267 84.6417999 - 0.27333 3454 selD,topB,ydjA 0.6695327163
150 nt 3246739 3246888 reverse yhaJ -4522 -56.00 - 0.4867 83.8035965 - 0.26000 4054 uxaA,uxaC 0.6671289802
150 nt 3883703 3883852 reverse purP -9513 -56.60 - 0.5200 84.5989990 - 0.28000 2029 dnaA,dnaN,recF 0.6626442075
150 nt 4395241 4395390 reverse yjfN -18720 -56.20 - 0.5267 84.9857025 - 0.29333 3229 queG 0.6626062393
150 nt 2664571 2664720 reverse hcaT -79 -56.20 - 0.5267 84.7899017 - 0.24666 3304 trmJ 0.6529098153
150 nt 2975533 2975682 reverse lysA -47 -57.20 - 0.5333 84.5955963 - 0.24666 1204 omrB 0.6521243453
150 nt 796718 796867 reverse ybhA -39 -58.40 - 0.5333 83.8794022 - 0.26666 2929 modE,modF 0.6405209899
150 nt 3288088 3288237 reverse rsmI -2330 -55.90 - 0.5067 83.9057007 - 0.28000 11479 agaR 0.6363855004
150 nt 3211791 3211940 reverse mug -1119 -56.10 - 0.5200 84.1829987 - 0.25333 3304 tsaD 0.6315983534
150 nt 2161503 2161652 reverse ogrK -3744 -55.70 - 0.5333 84.3114014 - 0.29333 10429 yegK,yegL 0.6064385772
150 nt 3284413 3284562 reverse rsmI -6005 -55.60 - 0.5333 84.2777023 - 0.25333 7804 agaR 0.6025381684
  1. Significant hits of the forward and reverse strands of the E. coli intergenic regions having high RND entropy (p-Val.<0.500), significantly low (p.Val. <0.050), GC and uracil compositions within the range of those for known riboswitches Threshold values and their corresponding p-values have been calculated separately for each genome-wide test. 50 nt overlap used for 100 nt scan (100090 segments). 175 nt overlap used for 150 nt scan (66414 segments). Distance from upstream and downstream operons are the distance from the center of the hit to the stop and start codons of upstream and downstream operons, respectively. Probability denotes the multinomial regression likelihood of being a riboswitch under the LMFEGCRND model. Positions are according to gbU00096.2 version of E. coli and not gbU00096.3 version. Negative values indicate distance to upstream operon. Columns Upsream/Downstream Operon show gene ID within the operon.
  2. 1Table 30: Complete list of genes in this operon is gspC,gspD,gspE,gspF,gspG,gspH,gspI,gspJ,gspK,gspL,gspM,gspO.
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