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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.