Skip to main content

Table 3 ChIP-chip signal ratios, PSSM scores, and predicted binding sites for ORFs enriched in the presence of σ 54

From: Use of a promiscuous, constitutively-active bacterial enhancer-binding protein to define the σ54 (RpoN) regulon of Salmonella Typhimurium LT2

Locus taga

Gene name

Signal ratiob

Orientationc

PSSMd

Start

End

Sequence

Sites located within intergenic regions:

STM0368

prpB

11

+

20.7

417914

417931

TGGCATAGCCTTTGCTTT

STM0448

clpP

4.6

+

14.6

503028

503045

TGTCACGTATTTTGCATG

STM0462

glnK

3.2

+

20.0

520445

520462

TGGCACATCCTTTGCAAT

STM0577

 

8.3

+

17.9

636883

636866

TGGCACGCCGTTTGCCAT

STM0649.S

 

6.9

+

18.7

711945

711962

TGGCACGCCTTTTGATTA

STM0665

gltI

3.2

+

22.1

730107

730090

TGGCACGTCTATTGCTTT

STM0830

glnH

16

+

20.8

897079

897062

TGGCATGATTTTTTCATT

STM1285

yeaG

4.1

+

21.5

1363884

1363867

TGGCATGAGAGTTGCTTT

STM1303

astC

4.0

+

21.7

1382105

1382122

TGGCACGAATGCTGCAAT

STM1690

pspA

23

+

20.3

1782486

1782469

TGGCACGCAAATTGTATT

STM2355

argT

3.5

+

16.2

2466359

2466376

TGGCATAAGACCTGCATG

STM2360

 

4.8

+

23.6

2472731

2472714

TGGCATGCCTTTTGCTTT

STM_R0152

glmY

31

+

20.6

2707874

2707857

TGGCACAATTACTGCATA

STM2809

proV

9.5

-

14.6

2955839

2955822

TGGCATGAATATTGCGAG

STM2840

 

6.5

+

20.1

2985009

2985026

TGGCACACTAGCTGCAAT

STM2843

hydN

23

+

17.1

2990721

2990704

TGGCACGATTCGTGTATA

STM2853

hycA

31

+

17.9

2999639

2999622

TGGCATGGAAAATGCTTA

STM2854

hypA

71

+

22.4

2999753

2999770

TGGCATAAATATTGCTTT

STM3521

rsr

15

+

21.2

3684734

3684717

TGGCACGCTGGTTGCAAT

STM3568

rpoH

22

+

18.9

3736836

3736819

TGGCACGGTTGTTGCTCG

STM3772

dgaA

3.6

+

20.3

3972484

3972467

TGGCACAACCTTTGCTCT

STM_R0167

glmZ

15

+

19.5

4141620

4141637

TGGCACGTTATGTGCAAT

STM4007

glnA

4.2

+

19.2

4217110

4217093

TGGCACAGATTTCGCTTT

STM4172

zraP

29

+

17.4

4388217

4388234

TGGCACGGAAGATGCAAG

STM4173

hydH

4.8

+

20.1

4388385

4388402

TGGCATGATCTCTGCTTA

STM4244

pspG

39

+

19.4

4465042

4465059

TGGCATGATTTTTGTAAG

STM4285

fdhF

10

+

18.2

4527564

4527547

TGGCATAAAACATGCATA

STM4367

yjeB

3.8

+

14.1

4610407

4610424

TGGCAGATATTTTGCTTG

STM4535

 

12

+

18.3

4794881

4794898

TGGCACGCCGCTTGCTCT

Sites located within the enriched ORF:

STM0131

ftsQ

7.6

+

6.2

153598

153615

TGGAACGCGTCTTGCAGG

STM0155

 

4.1

+

9.5

182767

182784

CGGCATGGCATTTGCCAG

STM0322

proA

7.8

-

11.3

368058

368041

CGGCACAGTTTATGCAAG

STM0332

 

3.0

-

8.1

376286

376269

TGGCCAGAAATATGCTTA

STM0526

ylbA

4.3

+

9.1

588233

588216

TGGCATTAATGCTGCATC

STM0699

 

14

+

13.7

761691

761674

TGGCATCGATATTGCAAA

STM0879^

potH

5.2

+

12.1

951550

951567

TGGCAGGAGTTTTTCAAT

STM0884

ulaA

5.2

+

10.0

955545

955562

CGGCACGATTTTTTCCAT

STM0901

 

3.9

+

11.7

971761

971778

TGGCATGAAACTTGTCAC

STM0940

 

9.5

+

13.7

1018097

1018080

TGGCCTGAATCTTGCTAA

STM0961

 

7.6

-

17.7

1041686

1041669

TGGCATGAAAGCTGCTCA

STM1361

ydiM

3.6

+

11.6

1443903

1443886

TGGCATTCTTTATGCTCA

STM1390

orf242

8.9

-

12.9

1475563

1475546

TGGCATCATTATTGCCTA

STM1409

ssaJ

5.0

+

6.5

1490273

1490290

TGGCATGAAGGTTCATCG

STM1586

 

6.6

-

13.5

1672845

1672862

TGGCAAGAATATTGCCAT

STM1594

srfB

4.8

+

13.4

1681565

1681582

TGGCACACGTTTTGCGCT

STM1665

 

4.2

-

11.7

1759185

1759168

TGGCATCATTTTTTCAAG

STM1904^

yecN

3.6

+

5.9

1998988

1999005

TGGCAAACCTGTGGTATA

STM1928

otsA

5.3

+

8.1

2023398

2023381

TGGCAGGAGCGTTTTATT

STM1990

yedA

5.6

+

14.4

2072998

2073015

TGGCGCGCTTTTTGCCTT

STM2033

cbiC

4.4

-

2.2

2111221

2111238

CGGTATAAATAATGCACG

STM2115

wcaA

4.3

-

9.5

2198775

2198792

TGGCATATAAATTGAGAT

STM2181

yohJ

15

+

4.9

2277993

2278010

AGGCATTTTTCTTGCATC

STM2430

cysK

4.8

-

11.7

2544207

2544190

TGGCATCACTGTTGCAGT

STM2475

 

9.0

-

1.0

2585621

2585638

TGGCACATCAGGCAAAAG

STM2476

ypfG

3.1

+

12.7

2586874

2586857

TGGCAGGTCACCTGCAAT

STM2517

sinH

4.6

-

11.1

2650462

2650479

TGGTACGGATCTTGCCAT

STM2563

yfhG

4.7

-

6.8

2705786

2705803

CGGCGTAATTTTTGCATC

STM2939

ygcH

10

+

10.9

3080061

3080044

CGGCACAGCTCTTGCATC

STM2957

rumA

5.5

+

14.5

3105809

3105792

TGGAACGCTTTTCGCATT

STM3072

 

4.1

-

6.9

3234181

3234164

TGGCCCATTGAATGCATC

STM3302

yhbE

5.5

+

12.6

3472042

3472025

TGGCATGATGGTCGCCAG

STM3535

glgA

8.0

+

11.6

3702315

3702298

AGGCATGTTTTATGCAAA

STM3721

rfaP

13.5

+

8.3

3916283

3916300

TGGTACGTAAAATGCACG

STM3863^

 

7.5

+

11.1

4072959

4072942

TGGCGCGATTATTGCCAG

STM3919

wzzE

4.2

+

11.0

4128295

4128312

TGGCCTGCTATTTGCCCT

STM3924

wecD

22

+

11.8

4133232

4133249

TGGCGCGGAAATTGCACA

STM4013.S

 

3.6

-

13.6

4222708

4222725

TGGCATAAAACCTGAAAA

STM4226

yjbA

6.4

-

4.2

4446318

4446301

AGGCGCGAATAATGCATC

STM4290

proP

13

+

10.1

4532022

4532039

TGGCCTGATTTTTGCAGG

STM4572

stjB

8.3

-

8.2

4826908

4826925

TGGCGTGGCGATTTCAAT

  1. aLoci listed in bold are known or predicted σ54-dependent promoters.
  2. bRatio of signals between WT and ΔrpoN cells.
  3. cOrientation of the predicted binding site with respect to the listed ORF. (+) binding site is in same direction as ORF; (−) binding site is in opposite direction as ORF.
  4. dPSSM score for the best predicted binding site within 1 kb of enriched ORF using the position-specific scoring matrix derived from the sequences in Additional file 2. As a reference to interpret the PSSM scores, the S. Typhimurium LT2 chromosome contains 3 sites with PSSM scores ≥22.0, 21 sites with PSSM scores ≥18.0, 61 sites with PSSM scores ≥14.0, and 401 sites with PSSM scores ≥10.0.
  5. ^The predicted binding site is a potential promoter for a neighboring gene based on its orientation and location within 250 bp of the 5’ end of a neighboring gene or a long intergenic region (>100 bp) that may encode a sRNA.
Back to article page

BMC Genomics

ISSN: 1471-2164

Contact us