Table 10 Candidate binding sites for the CO-responsive regulator CooA and the FNR/CRP-like HcpR factor
From: Reconstruction of regulatory and metabolic pathways in metal-reducing δ-proteobacteria
(a) CooA regulon | |||||
|---|---|---|---|---|---|
Gene | Operon | Function | Site | Position* | Score |
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 |