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Table 1 Summary of the datasets in RegulonDB

From: Evaluation of thresholds for the detection of binding sites for regulatory proteins in Escherichia coliK12 DNA

Regulatory protein

Number of binding sites

Site size (bp)

Regions with sites

Regions without sites

Ada

2

28

2

2

AlpA

-

-

-

1

AppY

-

-

-

2

AraC

15

17

5

1

ArcA

20

61

11

9

ArgR

12

16

6

1

AsnC

-

-

-

2

AtoC

-

-

-

1

BetI

2

21

2

-

BirA

2

40

2

-

CRP

109

19

65

15

CadC

-

-

-

1

Cbl

1

45

1

-

CsgD

-

-

-

2

CspA

3

5

1

1

CynR

2

60

2

-

CysB

7

42

5

1

CytR

12

40

6

2

DeoR

7

16

2

1

DnaA

8

9

2

-

DsdC

-

-

-

3

EbgR

-

-

-

1

EnvY

-

-

-

2

ExuR

-

-

-

1

FIS

29

16

25

-

FNR

30

22

20

4

FadR

6

17

4

-

FarR

2

21

1

-

FecI

1

7

1

1

FhlA

-

-

-

3

FruR

8

14

7

4

FucR

-

-

-

2

Fur

9

19

4

6

GalR

4

17

1

1

GalS

2

16

1

1

GatR

-

-

-

1

GcvA

4

29

2

-

GlpR

17

20

4

1

GntR

-

-

-

5

GutM

-

-

-

1

GutR

-

-

-

1

Hns

-

-

-

5

IHF

21

13

14

12

IclR

1

34

1

-

IlvY

4

26

2

-

KdpE

1

12

1

-

LacI

3

20

1

-

LeuO

-

-

-

1

LexA

9

20

8

1

Lrp

22

12

11

3

LysR

1

13

1

2

MalI

4

12

2

-

MalT

9

10

4

-

MarA

-

-

-

5

MarR

-

-

-

1

MelR

6

18

2

1

MetJ

5

8

2

1

MetR

3

24

2

1

Mlc

2

26

1

-

MtlR

-

-

-

1

NR_I

10

15

3

-

NadR

-

-

-

2

NagC

8

26

4

-

NarL

20

19

9

3

NhaR

-

-

-

1

OmpR

14

10

4

3

OxyR

4

45

4

-

PdhR

1

21

1

-

PhoB

7

17

4

1

PurR

16

16

14

3

RbsR

-

-

-

1

RcsB

2

25

2

-

RhaR

3

20

1

-

RhaS

3

17

2

-

Rob

-

-

-

4

SdiA

-

-

-

1

SoxR

2

19

2

-

SoxS

4

18

3

2

TdcA

1

15

1

-

TdcR

1

12

1

-

TorR

4

10

1

-

TrpR

5

27

5

-

TyrR

15

22

8

-

UhpA

1

39

1

-

XapR

2

13

1

-

XylR

4

16

2

-

  1. RegulonDB contains information for the 86 regulons shown in this table. Of these, only 60 have at least three known binding sites for their corresponding regulatory protein. The second column indicates the total number of known sites, which are distributed in upstream regions (fourth column). The last column indicates the number of upstream regions for which there is experimental evidence suggesting regulation, but no direct proof of binding of the regulator to the upstream site is yet available. For instance, there are 12 known sites for ArgR located in only six regions (with two sites per region), plus one region for a different gene for which there is evidence of regulation by ArgR.