Skip to main content

Table 2 Comparison of some typical regulons with our results

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

Regulon

Gene*

Cluster information†

Sequence of PCE‡

pyr operon (regulator: PyrR)

pyrR

34

AGTCCAGAGAGGCTGAGAAGGA-T

 

pyrP

34

AATCCAGAGAGGTTG

 

pyrB

C

CAGAGAGGCTT

S-box regulon (regulator: unknown)

metK

1,11

 
 

yusC

1

 
 

ykrW

1,5,11

 
 

yjcI

5,11

 
 

metE

5

 
 

ykrT

5,11

 
 

yitJ

5,11

 
 

cysH

B

 
 

yoaD

A

 
 

yxjG

A

 
 

yxjH

A

 

Hypothetical xanthine regulon (regulator: unknown)

purE

20

 
 

xpt

14,20

 
 

pbuG *

14

 

Aminoacyl-tRNA synthetases (regulator: uncharged tRNA)

serS

2

AGGGTGGCAACGCGAG

 

valS

2

AAAAAAGGTGGTACCGCGA

 

thrS

2

GAAAAAAGGGTGGAACCACGA

 

tyrS

2

TTAGTAGGGTGGTACCGCGA

 

leuS

2

AGGGTGGTACCGCGGG

 

tyrZ

2

AGGGTGGTACCGCGTG

 

ilvB

2

AGGGTGGTACCGCGGAAAG

 

pheS

2

AATAAGGGTGGTACCGCG

 

hisS

2

AACTAGGGTGGCACCACGGGTAT..

 

glyQ

2

GCAACTAGGGTGGAACCGCGGG

 

alaS

2

AGGGTGGTACCGCGAG-A

 

ileS

2

AGGGTGGTACCGCGAGA

 

proB

2

AAGGTGGTACCACGGA

 

cysE

D

C-AAACAGAGTGGAACCGCG

 

trpS

C

AGGGTGG

 

thrZ

A

 

Heat-shock regulon (regulator: CtsR)

ctsR

6

GTCAAATATAGTCAAAGTCA

 

clpE

6

GGTCAAAGATAGTCAAA

 

dnaJ *

6

GAAAGTCAAAGTCAGGCAT

 

clpP

B

 

CcpA regulon§ (regulator: CcpA)

bglS

47

TAGAAAACGCTTTCAA

 

msmX

47

GTAAACGCTTTCTT

 

yvfK

47

...TCTT-TAAAGCGCTTTCAT

 

mfd

47

GACCAAAGCGTTTTT

 

bglP

59

AAATGAAAGCGTTGACA

 

sucC

59

TATAGAATGAAAGCGC

 

mmgA

D

ATTGTAAGCGCT

 

hutP

D

AGTTAATAGTTATCAGA

 

rbsR

D

GTAAACGGTTACATAAACA

 

yxjC

B

 
 

ackA

B

 
 

licB

B

 
 

acuA

B

 
 

acsA

E

 
 

xylA

E

 
 

iolB

E

 
 

galT

E

 
 

uxaC

E

 
 

ydhO

E

 
 

acoA

E

 
 

araB

E

 
 

lcfA

E

 
 

dra

E

 
 

kdgA

E

 
 

yobO

E

 
 

treP

E

 
 

yxkJ

A

 
 

amyE

A

 
 

gntR

A

 
 

xynP

A

 
 

levD

A

 
 

dctP

A

 
 

citM

A

 
  1. *Probable new members identified by our analysis are shown with anasterisk. †Cluster number(s) are shown when available, otherwise, one of the situation codes is shown: A, orthologous genes not found; B, no overlaps between known binding site and PCE; C, PCE overlaps with known site but is too short; D, PCE overlaps with known site but is slightly different; E, binding site exists within the coding region. ‡PCE sequence in B. subtilis. The region overlapping with a known binding site is shown in bold. §CcpA-dependent genes identified by a systematic experiment [31] are not included.
Back to article page

Genome Biology

ISSN: 1474-760X

Contact us