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Table 23 Top classification hits in B. subtilis uracil-comp. constrained

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

R Start End Strand Upstream operon Upstream gene Dist. to upstream Uracil Dist. to downstream Downstream gene Downstream operon Probability
1 4134175 4134331 reverse BSU40230 yydA -182 0.3439 79 yydB BSU40220 0.931
2 3714883 3715039 forward BSU36030 ywrK -859 0.3949 2277 cotG BSU36070 0.922
3 3866327 3866483 reverse BSU37690 ywfG -1881 0.3503 79 eutD BSU37660 0.903
4 681153 681309 forward BSU06260 ydjN -201 0.3885 5731 yeaB BSU06320 0.899
5 1680274 1680430 forward BSU16080 ylqH 63 0.3822 79 sucC BSU16090 0.897
6 2316268 2316424 reverse BSU22040 ypbQ -99 0.363 236 ypbR BSU22030 0.896
7 688027 688183 forward BSU06320 yeaB -114 0.3885 79 yeaC BSU06330 0.893
8 243578 243734 forward BSU02170 ybfB -5370 0.363 236 purT BSU02230 0.89
9 984466 984622 reverse BSU09120 yhcK -1189 0.3885 79 cspB BSU09100 0.889
10 3421066 3421222 reverse BSU33340 sspJ -320 0.3312 79 lysP BSU33330 0.885
11 1493630 1493786 forward BSU14230 ykuV -230 0.3503 79 rok BSU14240 0.879
12 2531945 2532101 forward BSU24210 yqiG -14308 0.3439 9028 yqhQ BSU24490 0.879
13 300673 300829 forward BSU02770 yccK -1196 0.3822 79 ycdB BSU02790 0.875
14 4139318 4139474 forward BSU40240 yycS -3475 0.3567 864 rapG BSU40300 0.865
15 3681213 3681369 forward BSU35670 gtaB -14627 0.363 79 tagA BSU35750 0.864
16 3671690 3671846 reverse BSU35700 tagH -1795 0.3694 393 ggaA BSU35690 0.859
17 191850 192006 forward BSU01590 ybaS -12186 0.3057 2277 trnSL-Glu2 BSU_tRNA_75 0.856
18 20723 20879 forward BSU00120 yaaE -86 0.3185 79 serS BSU00130 0.856
19 2691445 2691601 reverse BSU26240 yqaO -1121 0.3439 79 yqaQ BSU26220 0.852
20 3158851 3159007 reverse BSU30890 ytxO -328 0.363 3376 ytdA BSU30850 0.852
21 1958206 1958362 forward BSU18190 yngC -9863 0.3949 44353 iseA BSU18380 0.852
22 557716 557872 forward BSU05100 yddT -188 0.3503 79 ydzN BSU05109 0.851
23 3907629 3907785 reverse BSU38100 ywcH -2594 0.3567 393 ywcI BSU38080 0.851
24 1926523 1926679 forward BSU17950 yneJ -1482 0.3949 79 citB BSU18000 0.851
25 1017271 1017427 forward BSU09400 spoVR -139 0.363 1649 lytE BSU09420 0.85
26 2769617 2769773 reverse BSU27160 cypB -4194 0.3185 1021 yrhP BSU27100 0.849
27 2739991 2740147 reverse BSU26830 yrpE -1287 0.3694 3533 aadK BSU26790 0.849
28 644384 644540 forward BSU05940 gcp -7 0.3694 2120 moaC BSU05960 0.848
29 2203622 2203778 forward BSU20580 yoqM -7279 0.363 79 yopS BSU20780 0.847
30 3014345 3014501 reverse BSU29460 moaB -90 0.3694 79 argG BSU29450 0.847
31 749147 749303 forward BSU06780 yeeC -3069 0.363 550 yeeG BSU06820 0.846
32 665425 665581 forward BSU06130 ydjC -677 0.3439 1963 gutB BSU06150 0.846
33 2106272 2106428 reverse BSU19360 odhB -1154 0.3949 79 yocR BSU19340 0.846
34 226409 226565 forward BSU02050 ybdO -82 0.3885 79 ybxG BSU02060 0.844
35 2106333 2106489 forward BSU19330 sodF -1353 0.3885 79 yocS BSU19350 0.844
36 308175 308331 forward BSU02840 ycdG 48 0.3503 79 adcA BSU02850 0.843
37 2678925 2679081 forward BSU26050 yqdB -427 0.363 12639 yqaP BSU26230 0.843
38 3875571 3875727 reverse BSU37760 rocC -130 0.3121 79 ywfA BSU37750 0.843
39 2433680 2433836 reverse BSU23340 ypuB -384 0.3885 236 ypzJ BSU23328 0.843
40 1533806 1533962 forward BSU14610 pdhD -445 0.3503 236 ykzW BSU14629 0.841
41 368137 368293 forward BSU03360 yciC -802 0.3312 1021 yckC BSU03390 0.841
42 447000 447156 forward BSU03930 gdh -792 0.3121 2120 ycnL BSU03970 0.84
43 2065804 2065960 forward BSU18960 yozM -348 0.3758 8557 yobN BSU19020 0.839
44 45296 45452 reverse BSU01550 gerD -113140 0.3822 236 abrB BSU00370 0.837
45 2048779 2048935 reverse BSU18810 yobA -1092 0.363 550 yoaZ BSU18790 0.836
46 3153718 3153874 reverse BSU30850 ytdA -938 0.3439 79 menF BSU30830 0.836
47 3388260 3388416 reverse BSU33040 fumC -685 0.3312 393 yuzO BSU33029 0.834
48 205252 205408 forward BSU01820 adaB -283 0.3248 79 ndhF BSU01830 0.834
49 469269 469425 forward BSU04160 mtlR 24 0.3121 79 ydaB BSU04170 0.834
50 1868460 1868616 forward BSU17360 ymzA -7 0.3885 79 nrdI BSU17370 0.834
51 3746069 3746225 forward BSU36380 rapD -577 0.3822 2905 ywoH BSU36440 0.833
52 3467327 3467483 reverse BSU33800 opuCD -140 0.3376 79 sdpR BSU33790 0.832
53 1903262 1903418 reverse BSU17690 yncM -170 0.3822 1963 cotU BSU17670 0.831
54 1017114 1017270 forward BSU09400 spoVR 18 0.3376 1806 lytE BSU09420 0.831
55 2709577 2709733 reverse BSU26490 yrkJ -346 0.3503 236 yrkK BSU26480 0.829
56 955738 955894 forward BSU08780 ygaJ -74 0.3822 79 thiC BSU08790 0.828
57 1283149 1283305 forward BSU12100 yjeA -539 0.3758 236 yjfC BSU12130 0.827
58 3988764 3988920 reverse BSU38860 galE -1105 0.293 79 yxkD BSU38840 0.825
59 200120 200276 forward BSU01770 glmM -198 0.2611 79 glmS BSU01780 0.825
60 2186812 2186968 reverse BSU20420 yorD -94 0.2611 79 yorE BSU20410 0.825
61 2926840 2926996 reverse BSU28630 pheT -89 0.3185 1021 yshA BSU28610 0.823
62 2054401 2054557 reverse BSU18840 xynA -119 0.3822 550 pps BSU18830 0.822
63 610963 611119 reverse BSU05660 ydgI -1149 0.3121 2277 dinB BSU05630 0.822
64 3457144 3457300 reverse BSU33700 opuBD -2583 0.3185 707 yvzC BSU33650 0.821
65 736435 736591 reverse BSU06740 yefB -2481 0.3376 3690 yerO BSU06700 0.82
66 2061478 2061634 reverse BSU18930 yobH -1953 0.3439 864 yozJ BSU18900 0.82
67 3268477 3268633 forward BSU31810 yuzE -4174 0.3949 8400 yukF BSU31920 0.82
68 3107044 3107200 forward BSU30340 ytvA 30 0.2675 1492 yttA BSU30360 0.82
69 2262616 2262772 reverse BSU21440 bdbB -2530 0.3885 15151 youB BSU21329 0.819
70 4118717 4118873 reverse BSU40110 bglA -2370 0.3758 5574 glxK BSU40040 0.818
71 4204755 4204911 reverse BSU40960 parB -722 0.3949 393 yyaD BSU40940 0.818
72 252357 252513 forward BSU02320 ybfP 36 0.3822 79 ybfQ BSU02330 0.818
73 3648264 3648420 reverse BSU35530 tagO -311 0.363 1806 degS BSU35500 0.818
74 850053 850209 forward BSU07750 yflA -3789 0.3694 236 treP BSU07800 0.817
75 255279 255435 forward BSU02330 ybfQ -1718 0.2994 2434 ybgA BSU02370 0.816
76 1541729 1541885 forward BSU14680 ykzC -2958 0.3376 79 ylaA BSU14710 0.816
77 909862 910018 forward BSU08330 yfiN -658 0.3503 79 estB BSU08350 0.816
78 4109617 4109773 reverse BSU40030 yxaB -1253 0.3885 79 yxaD BSU40010 0.813
79 3252983 3253139 forward BSU31660 mrpG -538 0.3949 4632 yuzC BSU31730 0.811
80 4066294 4066450 reverse BSU39600 yxeC -234 0.3567 864 yxeF BSU39570 0.81
81 1923077 1923233 forward BSU17910 yneF -231 0.3248 79 ccdA BSU17930 0.809
82 1540787 1540943 forward BSU14680 ykzC -2016 0.3503 1021 ylaA BSU14710 0.809
83 3665472 3665628 forward BSU35650 lytR -1192 0.3376 79 gtaB BSU35670 0.808
84 1679031 1679187 reverse BSU17060 ymzD -101508 0.3503 7458 ylqB BSU15960 0.808
85 2698717 2698873 reverse BSU26360 yqaD -714 0.363 79 yqaF BSU26340 0.808
86 3604725 3604881 reverse BSU35100 yvlD -1958 0.363 236 yvmC BSU35070 0.808
87 3354671 3354827 forward BSU32650 yurS -105 0.3057 17820 yuzL BSU32849 0.807
88 3052234 3052390 forward BSU29710 acuC -9600 0.3503 2434 ytoQ BSU29850 0.806
89 188867 189023 forward BSU01590 ybaS -9203 0.3185 5260 trnSL-Glu2 BSU_tRNA_75 0.806
90 245389 245545 reverse BSU02340 gltP -8050 0.363 1806 ybfI BSU02220 0.805
91 1445373 1445529 reverse BSU13810 ykvS -2210 0.3439 2748 ykvN BSU13760 0.804
92 2249114 2249270 reverse BSU21440 bdbB -16032 0.3439 1649 youB BSU21329 0.803
93 3918262 3918418 reverse BSU38190 galT -752 0.3057 79 qoxA BSU38170 0.801
94 933760 933916 reverse BSU08620 yfhP -618 0.3439 5574 sspK BSU08550 0.8
95 201248 201404 reverse BSU01800 alkA -1220 0.293 7301 ybbK BSU01720 0.8
96 3684268 3684424 reverse BSU35780 lytD -479 0.3439 3376 tagD BSU35740 0.8
97 2739834 2739990 reverse BSU26830 yrpE -1444 0.3439 3376 aadK BSU26790 0.799
98 2252097 2252253 reverse BSU21440 bdbB -13049 0.3949 4632 youB BSU21329 0.798
99 1601271 1601427 reverse BSU15640 yloA -34781 0.3503 24100 ylbP BSU15100 0.797
100 2111609 2111765 reverse BSU19380 yojO -149 0.3439 79 sucA BSU19370 0.796
  1. Top 50 hits of the forward and reverse strands of the B. subtilis intergenic regions using no-overlap 157 nt window and under the LMFEGCRND model. Uracil composition constrained to that of the range of known riboswitches in B. subtilis (between 0.2484 and 0.40127). 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.
  2. Interesting hits are shown in bold.
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