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Table 1 Selected data about investigated transcription factor binding sites

From: In silico simulations of occurrence of transcription factor binding sites in bacterial genomes

Protein

Genome

Motif length

# of sites

Information content

ΔNgenome

ΔNig

ΔNcod

ΔNtem

AraC

E. coli

17

15

12.1

4

6

0

1

ArcA

E. coli

17

77

9.9

1

5

0

0

ArgP

E. coli

18

16

11.3

2

3

2

0

ArgR

E. coli

18

29

15.7

8

10

0

0

CpxR

E. coli

14

58

9.0

2

3

1

0

Cra

E. coli

16

42

14.7

2

14

0

0

Crp

E. coli

22

260

11.3

28

55

1

3

CsgD

E. coli

17

24

8.4

1

2

0

1

CytR

E. coli

18

18

11.3

1

2

1

0

DnaA

E. coli

11

14

13.0

0

8

0

0

FadR

E. coli

18

16

15.6

5

12

0

2

Fis

E. coli

15

214

6.9

0

3

0

0

FlhDC

E. coli

16

16

12.8

2

13

1

0

Fnr

E. coli

14

84

11.1

4

10

0

0

Fnr

R. sphaeroides

14

27

17.1

18

38

0

1

Fur

E. coli

18

48

15.8

9

27

1

1

GadW

E. coli

20

17

14.5

1

5

0

0

GadX

E. coli

21

24

11.3

2

5

0

0

GalR

E. coli

15

12

16.3

3

9

0

2

GlpR

E. coli

19

17

15.3

3

5

1

0

H-NS

E. coli

13

48

8.2

0

0

0

1

IHF

E. coli

13

95

8.4

0

4

0

3

LexA

C. difficile

16

17

15.4

1

0

0

0

LexA

E. coli

20

40

17.9

24

36

0

1

LexA

M. tuberculosis

18

23

22.5

21

24

2

3

Lrp

E. coli

15

80

7.1

0

3

0

1

MalT

E. coli

10

15

12.0

0

3

0

0

MarA

E. coli

19

23

12.4

2

6

0

0

MetJ

E. coli

16

15

14.1

2

14

0

2

Nac

E. coli

17

14

10.6

1

2

0

0

NagC

E. coli

22

20

19.9

7

10

1

1

NarL

E. coli

17

67

7.8

0

5

0

0

NsrR

E. coli

14

39

12.2

0

1

0

0

NtrC

E. coli

18

25

14.4

5

9

0

0

OmpR

E. coli

19

20

13.5

3

4

0

1

OxyR

E. coli

20

34

11.2

0

2

1

1

PhoB

E. coli

22

24

13.4

4

9

1

0

PhoP

E. coli

17

33

12.0

4

4

2

1

PurR

E. coli

16

21

20.5

8

21

1

0

Rob

E. coli

17

13

14.2

3

7

0

0

σ54

S. enterica

18

53

16.9

3

4

1

0

SoxS

E. coli

18

27

12.5

3

7

0

0

TyrR

E. coli

17

19

15.8

6

7

0

0

  1. The DNA-binding proteins investigated in this work are listed together with the length of the motif in nucleotides, number of sites in the training set, and motif information content (in bits). ΔNgenome is the number of sites found in the genome that have higher PSSM score than the highest score expected to be found in the random sequence (median value among the 1000 simulations). ΔNig is the analogous value when the search is restricted to intergenic sequences and ΔNcod and ΔNtem are the analogous values for the search restricted to codon and template strands of protein-coding genes, respectively