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Table 28 Top classification hits in E. coli uracil-comp. constrained

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

R Start End Strand Upstream operon Dist. to upstream Uracil Dist. to downstream Downstream operon Probability
1 3886253 3886352 reverse purP -6993 0.31 4549 dnaA,dnaN,recF 0.876
2 3181557 3181656 reverse ribB,sroG -229 0.33 1149 ygiD 0.865
3 3755951 3756050 reverse selA,selB -40 0.33 149 yiaY 0.861
4 3490370 3490469 reverse php,yhfS,yhfT,yhfU,yhfW,yhfX -12538 0.32 99 ppiA 0.854
5 4535630 4535729 forward yjhR -1527 0.31 3302 fimB 0.849
6 3497220 3497319 reverse php,yhfS,yhfT,yhfU,yhfW,yhfX -5688 0.33 6949 ppiA 0.849
7 3576850 3576949 reverse yhhW -74 0.33 149 gntK,gntR,gntU 0.844
8 2055603 2055702 reverse asnW -399 0.33 4299 yeeL_1,yeeL_2 0.843
9 2739273 2739372 reverse rimM,rplS,rpsP,trmD -2883 0.3 149 aroF,tyrA 0.842
10 2698570 2698669 reverse acpS,era,pdxJ,recO,rnc -21 0.31 399 shoB 0.84
11 3945101 3945200 reverse hdfR -1 0.3 5799 hsrA,yieP 0.835
12 2739223 2739322 reverse rimM,rplS,rpsP,trmD -2933 0.31 99 aroF,tyrA 0.832
13 3453521 3453620 reverse bfd,bfr -10701 0.32 149 gspA,gspB 0.825
14 4274265 4274364 reverse soxS -769 0.32 1249 yjcB 0.822
15 1467282 1467381 forward ydbA_1 -1259 0.32 52 insI-2 0.82
16 3116880 3116979 forward pheV -8368 0.33 2452 C0719 0.819
17 790896 790995 forward aroG -4939 0.26 3052 acrZ 0.817
18 2777069 2777168 forward yfjX,yfjY,yfjZ,ypjF,ypjJ -1216 0.33 7302 ygaQ_1,ygaQ_2 0.817
19 3189691 3189790 reverse glgS -21 0.31 6999 ribB,sroG 0.817
20 1694096 1694195 reverse uidR -341 0.33 49 uidA,uidB,uidC 0.815
21 2823699 2823798 reverse norR -5049 0.31 149 mltB 0.81
22 1805258 1805357 reverse yniB -1414 0.32 1199 ydiY 0.809
23 3382541 3382640 reverse yhcO -1289 0.33 299 mdh 0.809
24 1868697 1868796 reverse yoaI -3356 0.29 4249 mipA 0.808
25 2386449 2386548 reverse nuoA1 -1572 0.31 49 yfbN 0.807
26 3617057 3617156 reverse rbbA,yhhJ,yhiI -6596 0.3 7349 yhhS 0.806
27 2815604 2815703 forward micA -2660 0.29 8202 gutM,gutQ,srlA,srlB,srlD,srlE,srlR 0.805
28 2943865 2943964 reverse mltA -189 0.31 49 tcdA 0.804
29 1983499 1983598 forward uspC -5245 0.31 1402 ftnB 0.803
30 150155 150254 forward yadD -2236 0.32 11902 hrpB 0.801
31 2553093 2553192 forward amiA,hemF -898 0.33 3652 intZ 0.8
32 2876452 2876551 reverse cas1,cas2,casA,casB,casC,casD,casE -90 0.31 2149 cysC,cysD,cysN 0.8
33 1217949 1218048 reverse ymgD,ymgG -3530 0.33 3299 bluF 0.8
34 3346238 3346337 reverse elbB,mtgA -816 0.33 8199 mlaB,mlaC,mlaD,mlaE,mlaF 0.798
35 1174989 1175088 reverse ycfZ,ymfA -4664 0.3 649 ycfT 0.798
36 4298873 4298972 forward gltP -5007 0.26 12452 rpiB 0.797
37 585173 585272 forward appY -1471 0.29 9602 cusA,cusB,cusC,cusF 0.796
38 1397665 1397764 forward ynaJ -1970 0.32 5052 abgR 0.795
39 4492546 4492645 forward lptF,lptG -6074 0.29 52 idnK 0.795
40 655892 655991 reverse crcB -837 0.32 749 dcuC 0.795
41 266028 266127 reverse yafZ,ykfA -331 0.28 299 yafW2 0.795
42 2033559 2033658 reverse yedV,yedW -1210 0.32 2099 yedJ,yedR 0.794
43 3963904 3964003 reverse aslA -18422 0.32 299 rhlB 0.794
44 1463517 1463616 reverse insC-2,insCD-2,insD-2 -2379 0.33 11899 paaZ 0.794
45 2650116 2650215 forward xseA -16443 0.31 352 sseA 0.793
46 582654 582753 forward tfaX -322 0.3 202 appY 0.793
47 4076645 4076744 reverse fdhE,fdoG,fdoH,fdoI -1628 0.29 5099 yihS,yihT,yihU 0.793
48 2033409 2033508 reverse yedV,yedW -1360 0.32 1949 yedJ,yedR 0.793
49 1762598 1762697 forward lpp -6868 0.27 4452 ydiK 0.792
50 4501881 4501980 forward yjgZ -2220 0.32 152 yjhB,yjhC 0.792
51 1676251 1676350 forward tqsA -3231 0.33 152 ydgH 0.791
52 2166386 2166485 forward cyaR -1113 0.32 302 yegS 0.789
53 2429322 2429421 forward folX,yfcH -8650 0.28 6602 flk 0.789
54 4083889 4083988 forward yiiF -5848 0.29 102 fdhD 0.789
55 2491327 2491426 reverse yfdX -413 0.32 99 frc 0.789
56 1165025 1165124 reverse comR -2349 0.31 4299 fhuE 0.789
57 1933126 1933225 forward purT -2994 0.3 1502 yebK 0.787
58 1204407 1204506 reverse stfE,tfaE -3284 0.25 2299 ymfK 0.787
59 1493112 1493211 forward trg -929 0.32 152 ydcJ 0.786
60 1714050 1714149 forward gstA -995 0.31 3802 slyB 0.786
61 1397615 1397714 forward ynaJ -1920 0.32 5102 abgR 0.784
62 5034 5133 forward thrA,thrB,thrC,thrL 35 0.27 152 yaaX 0.784
63 4547775 4547874 reverse gntP -152 0.25 10299 nanC,nanM 0.784
64 2257385 2257484 forward yeiL -3300 0.3 4452 setB 0.783
65 660791 660890 forward tatE -2369 0.29 13402 ybeL 0.781
66 3945051 3945150 reverse hdfR -51 0.29 5749 hsrA,yieP 0.781
67 2238382 2238481 forward preA,preT -3811 0.33 3502 yeiG 0.779
68 925014 925113 reverse serW -44 0.31 3249 cspD 0.779
69 13587 13686 reverse hokC,mokC -3115 0.3 1849 yaaI 0.779
70 2734984 2735083 reverse aroF,tyrA -1937 0.33 999 rluD,yfiH 0.778
71 2880686 2880785 forward iap -4997 0.32 9502 queD 0.777
72 1078128 1078227 forward rutR -3976 0.29 352 putP 0.776
73 187962 188061 forward cdaR -4293 0.32 1702 rpsB,tff,tsf 0.776
74 497037 497136 reverse aes -1152 0.25 7049 priC,ybaM 0.776
75 3181662 3181761 forward zupT -268 0.3 1152 yqiC 0.775
76 593123 593222 forward appY -9421 0.29 1652 cusA,cusB,cusC,cusF 0.775
77 1250189 1250288 forward ycgY -5317 0.33 52 dhaR 0.775
78 3597882 3597981 reverse rpoH -21 0.32 249 livJ 0.775
79 117883 117982 forward guaC -3347 0.33 802 ampD,ampE 0.774
80 1073265 1073364 forward ymdF -5739 0.31 152 rutR 0.774
81 3416188 3416287 reverse alaU,ileU,rrfD,rrfF,rrlD,rrsD,thrV -5208 0.28 4749 envR 0.774
82 4238098 4238197 forward yjbE,yjbF,yjbG,yjbH -296 0.33 202 psiE 0.773
83 3313859 3313958 forward psrO -4390 0.32 2752 argG 0.773
84 238253 238352 reverse yafU -444 0.29 2299 rnhA 0.773
85 2627711 2627810 reverse guaA,guaB -1220 0.31 799 yfgF 0.773
86 4156263 4156362 forward argB,argC,argH 32 0.3 202 oxyR 0.772
87 58274 58373 forward djlA -46 0.32 152 yabP,yabQ 0.772
88 3108528 3108627 reverse yghD,yghE -35 0.33 1399 speC 0.772
89 2750731 2750830 reverse ratA,ratB -1250 0.31 2049 grpE 0.772
90 454057 454156 forward bolA 5 0.32 252 tig 0.771
91 573621 573720 forward ybcQ -10 0.26 2952 essD,rrrD,rzpD 0.771
92 905496 905595 forward amiD,ybjQ -481 0.31 10152 ybjD 0.771
93 2407114 2407213 reverse yfbS -379 0.32 2499 lrhA 0.771
94 1733426 1733525 reverse ydhP -670 0.31 1349 grxD 0.771
95 604509 604608 forward pheP -1902 0.33 2502 hokE 0.77
96 1431895 1431994 forward lomR_2,stfR,tfaR -836 0.31 3202 micC 0.77
97 1395289 1395388 forward insH-4 -124 0.28 52 ynaJ 0.769
98 253317 253416 forward dinB,yafN,yafO,yafP -107 0.3 102 prfH,ykfJ 0.768
99 573571 573670 forward ybcQ 40 0.28 3002 essD,rrrD,rzpD 0.768
100 3986826 3986925 forward glmZ -2151 0.32 2302 cyaA 0.768
  1. Top 50 hits of the forward and reverse strands of the E. coli intergenic regions that have uracil composition within the range of known riboswitches in E. coli (between 0.23 and 0.34). 50 nt-overlap 100 nt window used. The ranking of each hit is denoted in column R. 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.
  2. 1Table 28: Complete list of genes in this operon is nuoA,nuoB,nuoC,nuoE,nuoF,nuoG,nuoH,nuoI,nuoJ,nuoK,nuoL,nuoM,nuoN. 2Table 28: Complete list of genes in this operon is yafW,yafX,yafY,ykfB,ykfF,ykfG,ykfH,ykfI.
  3. Interesting hits are shown in bold.