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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
  1. *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.