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Table 1 Correspondence between known transcription factor binding sites and PCEs

From: Prediction of co-regulated genes in Bacillus subtilis on the basis of upstream elements conserved across three closely related species

Factor name

Orthologs*

Number of known sites†

Number of sites to be detected‡

Number of overlaps§

AbrB

H S

11 (1)

7

3

AhrC

H S

5 (1)

3

2

AraR

H

5 (1)

2

1

BirA

H S

1

0

-

BltR

H

1

1

0

BmrR

None

1

0

-

CcpA

H S

33 (17)

11

6

CodY

H S

2

1

1

ComA

None

5

2

0

ComK

None

1

0

-

CtsR

H S

6

6

4

DegU

H S

14 (3)

5

1

DeoR

H

1

1

0

LexA

H

8

6

3

ExuR

S

1

1

0

Fnr

H

2

2

1

GerE

H S

21 (2)

7

0

GlnR

S

6

3

0

GltC

H S

3

3

0

GltR

None

4

2

0

GntR

None

1

0

-

Hpr

H

8 (1)

3

0

HrcA

H S

2

2

2

IolR

None

2

1

0

LevR

S

3

0

-

LicT

H

1

1

1

LrpC

H

1

1

0

Mta

H S

3

2

1

MtrB

H S

1

1

0

PhoP

H S

6 (2)

2

0

PyrR

H S

3

3

3

PurR

H S

1

0

-

RibC

H S

1

0

-

RocR

H

4

2

0

SacT

None

1

0

-

SacY

None

1

0

-

SenS

None

1

0

-

SinR

H

6

5

5

Spo0A

H S

22 (1)

18

10

SpoIIID

H S

12 (5)

6

2

TnrA

H S

10

6

1

TreR

H S

2

2

2

Xre

H

4

0

-

XylR

H S

1

1

1

MntR

H S

2

1

1

Zur

H S

2

2

1

Total

 

232 (34)

122

52

  1. *Name(s) of species having the orthologous gene with the B. subtilis gene. H: B. halodurans; S: B. stearothermophilus.†Total number of experimentally verified binding sites of < 50 bp. The number of binding sites in the coding region is shown in parentheses. ‡Number of known binding sites in the region analyzed in this work. §Number of analyzed sites overlapping with PCEs over 5 bp.
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Genome Biology

ISSN: 1474-760X

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