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Table 2 Candidate ARG boxes upstream of arginine metabolism related genes and operons

From: Conservation of the binding site for the arginine repressor in all bacterial lineages

Genome

Operon

Position

Score

Site

E. coli

argR

-64

4.24

ttTGcATAAAAATTCATc

  

-43

3.34

tATGcAcAAtAATgttgT

 

argA

-50

3.98

AcaGAATAAAAATaCAcT

  

-39

3.98

ttcGAATAAtcATgCAaa

 

argCBH

-128

4.61

tATcAATAttcATgCAgT

  

-109

4.61

tATGAATAAAAATaCAcT

 

argD

-68

4.01

AgTGAtTttttATgCATa

  

-47

3.50

tgTGgtTAtAAtTTCAca

 

argE

-64

3.80

AgTGtATttttATTCATa

  

-43

3.39

AcTGcATgAAtATTgATa

 

argF

-65

4.16

AATGAATAAttAcaCATa

  

-44

4.41

AgTGAATtttAATTCAaT

 

argG

-210

4.31

tgTGAATgAAtATcCAgt

  

-91

3.90

AtTaAATgAAAAcTCATT

  

-70

4.51

ttTGcATAAAAATTCAgT

 

argI

-63

4.33

AATGAATAAtcATcCATa

  

-42

4.49

AtTGAATtttAATTCATT

 

carAB

-50

4.36

tgTGAATtAAtATgCAaa

  

-39

3.79

AgTGAgTgAAtaTTCtcT

 

artPIQM

-72

4.08

AtTGaATAAttATTCtgT

 

artJ

-86

4.36

AtTGcATAtAAATTCAcT

H. influenzae

HI1209

-50

4.27

AgTGAATttttATgCAaT

 

HI0811

-54

4.52

tATGAATAAAtATgCAca

 

HI1727

-64

3.87

AtaGAATttttATTCAca

  

-43

3.75

AtcGAtTAtttATTCAaT

 

HI1180-77

-50

4.01

tATGcATAAAAATgtAaT

V. cholerae

VC2316

-15

3.82

AaaGAATAAAAAgTCATT

 

VC2390-89

-52

3.57

ttTGcAaAAtAATTtATT

 

VC2508

-72

3.72

ttaaAATAtttATTCAcT

  

-51

3.35

AtaGcATtttcATgCtTT

 

VC2618

-120

3.83

AaTaAATgtAAATaCAaT

 

VC2644-42

-76

3.00

AacacATAttAAaTCAcT

  

-55

4.00

AGTGAATAAAAAaaCAaT

 

VC2645

-79

3.50

AtTGttTttttATTCAcT

  

-58

3.27

AGTGAtTtAAtATgtgTT

 

VCA0757-60

-74

3.00

ttTtggTttttATaCATT

  

-53

3.85

AtTGcATAAAAATaCgTT

B. subtilis

argCJBD

-64

5.22

ATtAATTTtTATTCAT

 

carABargF

-55

4.54

AgGcATAaAAATTCAT

  

-35

4.02

AtaAtTAatTATTCAT

 

argGH

-67

5.04

ATGtATTTtTATTaAa

 

yqjN

-31

4.54

AaGcATTTtTATTCAT

  

-47

4.91

ATttATTTtTATaCAa

 

rocABC

-53

5.14

tTGcATTTtTATTCAT

 

rocDEF

-63

4.76

tTGcATTTATATaaAg

 

rocR

-193

4.76

cTttATATAAATgCAa

 

yqiXYZ

-88

4.21

tTGcATAaAAATgaga

  

-51

4.62

AcGAATAaATATTCAa

C. acetobutylicum

414

-191

5.27

ATGAATAaATATTCAa

 

491

-132

4.62

tTGAATAaATATTCgT

  

-32

5.27

ATGAATAaAAATTCAa

 

1203-4

-124

5.04

ATGAATATtTATaaAa

 

2787-8

-63

4.79

tTGAATATtTATaaAg

  

-43

4.59

gTGtATAatTATTCAT

 

2786-2785

-118

4.59

ATGAATAatTATaCAc

  

-98

4.79

cTttATAaATATTCAa

 

3090-89

-181

4.96

ATGcATAaATATaaAT

  

-80

4.91

ATGtATAaATATaaAa

 

3533

-87

4.96

ATGcATAaATATaaAT

  

-67

4.89

tTGAATAatTATaaAa

 

4268-65

-194

5.09

ATGcATAaATATTaAT

  

-69

4.62

gTtAATAatTATTCAT

T. maritima

TM0371

-59

4.21

tTtcATATtTATgCta

 

TM0558-57

-81

3.92

tTtAATTcAAAgTaAa

 

TM0593-91

-34

4.16

tTGtgTTatAATaaAT

 

TM1780-85

-138

3.87

cgtAATTgATATTCAT

 

TM1873

-91

4.44

ATttATTTAAcTTaAT

D. radiodurans

DR0080

-57

4.11

cTGtATTTcTATaCAg

 

DR0674-78

-131

4.09

tTGcATAgtcATTCAT

 

DR2610

-85

3.62

ATGgATTgAAATcCAg

  

-62

3.69

cTGgATTTtAAggaAT

C. pneumoniae

glnPQ

-53

4.26

tTGcATAaATATgatT

  

-32

4.64

ATaAATAaATATgCAT

 

artJ

-112

3.92

tTtAATcaAAATTatT

  

27

3.96

ATttATTTtTATaatg

M. tuberculosis

Rv1652-59

-11

3.91

tTGcATAacgATgCAa

  1. Position is indicated relative to the start of translation. The score for E.coli and H. influenzae genes was computed using the profile from [27]; other scores were computed using the profile trained on B. subtilis candidate ARG boxes using the procedure from [28]. The sites used to construct the profile are shown in bold.