Table 10 |
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|
Candidate binding sites for the CO-responsive regulator CooA and the FNR/CRP-like HcpR factor |
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|
Gene |
Operon |
Function |
Site |
Position* |
Score |
|
|
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|
(a) CooA regulon |
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|
Desulfovibrio vulgaris |
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|
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 |
|
|
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|
*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. |
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|
Rodionov et al. Genome Biology 2004 5:R90 doi:10.1186/gb-2004-5-11-r90 |
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