Table 10

Candidate binding sites for the CO-responsive regulator CooA and the FNR/CRP-like HcpR factor

Gene

Operon

Function

Site

Position*

Score


(a) CooA regulon

Desulfovibrio vulgaris

207573

cooSC

CO dehydrogenase (CODH)

TGTCGGCTAGCCGACA

-187

6.04

207772

cooMKLXUHXF

CODH-associated hydrogenase

gGTCGGtcAaCCaACt

-64

4.43

Desulfovibrio desulfuricans

393975

cooSC

CO dehydrogenase (CODH)

TGTCaGCcAGCCGACA

-111

5.78

(b) HcpR regulon

Desulfovibrio vulgaris

208467

Two-component response regulator

TTGTGAcATgTaTaACAA

-74

5.61

206736

sat

ATP sulfurylase

TTGTaAAtTtTTTCACAA

-148

5.53

206272

apsAB

APS reductase

TTGTtAAtTccaTCACAA

-168

5.29

209106

phcAB

Putative thiosulfate reductase

aTGTGAcgcATTTCgCAA

-194

5.06

207772

cooMKLXUHXF

CODH-associated hydrogenase

TTGgGAAtcgaTTCACAA

-116

4.97

208738

208738-208737

Two-component regulatory system

cTGTGAAAcATgTCgCAt

-104

4.88

206515

206515-206516

Putative sulfite/nitrite reductase, polyferredoxin

gTGTGAcccgcgTCACAg

-52

4.79

209119

Hypothetical protein conserved in Archaea

TTGTtcAcaAaaTCACAA

-218

4.61

208040

hcp-frdX-adhE-208043

Hybrid cluster-containing protein, ferredoxin, alcohol dehydrogenase, histidine kinase

aTtTGAcgcAcgTCACAA

-179

4.55

Desulfovibrio desulfuricans

392869

209119

Hypothetical protein conserved in Archaea

TTGTtAAATAaTTCACAA

-118

5.93

395578

apsAB

APS reductase

TTGTtAAATATcTCACAA

-186

5.77

394579

sat

ATP sulfurylase

TTGctAAAaATTTCACAA

-147

5.43

TTGTtAcAatTaTCACAt

-328

4.93

393955

Two-component response regulator

TTGTGAcAgcTgTCACAA

-80

5.36

393201

Two-component response regulator

TTGTGAAggAaaTaACAA

-18

5.29

392939

~ 6-aminohexanoate-cyclic-dimer hydrolase

TTGTtAAtTATTTaAaAA

-61

5.00

395499

395499-395498-395497-395496

Arylsulfatase, thioredoxin, thioredoxin reductase, sulfate transporter homolog

aTGTGAAAaAcaTCACAt

-129

4.98

393758

393758-..-393776

Large gene cluster encoding carboxysome shell proteins, aldehyde dehydrogeanses, ...

TTGTtAtATtTTTCtCAA

-148

4.97

394469

394469-394470

Putative sulfite/nitrite reductase, polyferredoxin

aTGTGAccTgcaTCACAg

-81

4.86

394261

hcp-frdX-uspA

Hybrid cluster-containing protein, ferredoxin, universal stress protein UshA

TTGTGActccggTCACAt

-152

4.81

395604

phcAB

Putative thiosulfate reductase

TTGTGcttTtTTgCACAA

-114

4.25

Desulfotalea psychrophila

425344

frdX

Ferredoxin

ATTTGAtCTAGGTCAAAg

-103

5.81

423439

hcp3/hcp2

Hybrid cluster-containing proteins

ccTTGACCTgGGTCAAtT

-200

5.47

422894

hcp1

Hybrid cluster-containing protein

tcTTGACtTAGGTCAAAg

-117

5.44

Desulfuromonas species

389812

hcp1/?-frdX2-?

Hybrid cluster-containing protein/ferredoxin

ATTTGACCTcGGTCAAga

-155

5.66

AcaTGACgcAGaTCAAAa

-200

4.87

389024

hcp3

Hybrid cluster-containing protein

tcTTGAtCTgGaTCAAAT

-85

5.45

391271

dnrA

~ Regulator of NO signaling

cTTTGACCcgGGTCAAtT

-109

5.44

390920

hcp2

Hybrid cluster-containing protein

ATTTGACCTgGGTCAtgT

-127

5.40

390344

galE

~ Nucleoside-diphosphate-sugar epimerase

ATTTGACCccGGTCAAta

-117

5.39

392163

yccM

Polyferredoxin

AaaTGACCcAGGTCAAAg

-80

5.14

392663

Two-component response regulator

AaTTGAttcAGGTCAAgg

-85

5.06

390999

Cytochrome c (heme-binding protein)

ATTTGACggccGTCAAAg

-83

5.02

390998

frdX1

Ferredoxin

tTTTGAtgccGGTCAAgg

-96

5.00

388470

hcp4

Hybrid cluster-containing protein

tTTTGAttTgtaTCAAtT

-126

4.66


*Position relative to the start of translation. (a) Candidate sites of the CO-responsive regulator CooA in Desulfovibrio species; (b) candidate sites of the FNR/CRP-like HcpR factor regulating energy metabolism. Lower case letters represent positions that do not conform to the consensus sequence.

Rodionov et al. Genome Biology 2004 5:R90   doi:10.1186/gb-2004-5-11-r90

Open Data