RegulonDB RegulonDB 11.2:Regulon Page
   

FNR DNA-binding transcriptional dual regulator

Synonyms: FNR, FNR-[4Fe-4S]2+ reduced, FNR-[2Fe-2S]2+ oxidized
Summary:
FNR is the primary transcriptional regulator that mediates the transition from aerobic to anaerobic growth through the regulation of hundreds of genes. Generally, this protein activates genes involved in anaerobic metabolism and represses genes involved in aerobic metabolism [4, 99, 108]. FNR also regulates the transcription of many genes with other functions, such as acid resistance, chemotaxis, cell structure, and molecular biosynthesis, among others [4, 99]. The cellular concentration of FNR is similar under both anaerobic and aerobic growth [109], but its activity is regulated directly by oxygen. A binding signature from FNR was observed only in low oxygen conditions [108]. Under anaerobiosis, FNR acquires a [4Fe-4S] cluster that causes a conformational change and dimerization of the protein that causes it to become activated [110].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
FNR Functional   nd nd nd
FNR-[2Fe-2S]2+ oxidized Non-Functional Covalent Apo nd nd nd
FNR-[4Fe-4S]2+ reduced Functional Covalent Holo nd nd nd
Evolutionary Family: CRP
TFBs length: 14
TFBs symmetry: inverted-repeat
Sensing class: Using internal synthesized signals
Connectivity class: Global Regulator
Gene name: fnr
  Genome position: 1398774-1399526
  Length: 753 bp / 250 aa
Operon name: fnr
TU(s) encoding the TF:
Transcription unit        Promoter
fnr
fnrp


Regulon       
Regulated gene(s) aceE, aceF, ackA, acnA, acrE, acrF, adhE, aer, aldA, amtB, ansB, arcA, aspA, aspC, bcsB, bcsZ, cadC, caiA, caiB, caiC, caiD, caiE, caiF, caiT, ccmA, ccmB, ccmC, ccmD, ccmE, ccmF, ccmG, ccmH, ccp, cheB, cheR, cheY, cheZ, citC, citD, citE, citF, citG, citX, cydA, cydB, cydC, cydD, cyoA, cyoB, cyoC, cyoD, cyoE, cysG, dcuA, dcuB, dcuC, dcuR, dcuS, dmsA, dmsB, dmsC, dmsD, dpiA, dpiB, dppA,
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Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
membrane (79)
anaerobic respiration (65)
aerobic respiration (27)
electron donors (26)
electron acceptors (24)
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Regulated operon(s) ackA-pta, acrEF, adhE, aer, aldA, ansB, arcA, aspA-dcuA, aspC, bcsABZC, cadC, caiF, caiTABCDE, ccp, citCDEFXG, cydAB, cydDC, cyoABCDE, dcuB-fumB, dcuC, dcuSR, dmsABC, dpiBA, dppABCDF, emrKY, fdhF, fdnGHI, feoABC, fes-ybdZ-entF-fepE, fixABCX, fnr, fnrS, focA-pflB, frdABCD, fumAC, gadAXW, garPLRK-rnpB, gcvTHP, gdhA, glnK-amtB, glpABC, glpTQ, gltBDF, gnd, grcA, hcp-hcr-poxB-ltaE-ybjT, hemA-prfA-prmC, hlyE, hmp, hyfABCDEFGHIJR-focB, hypABCDE-fhlA, iraM, katG, malPQ, map-glnD-dapD, moaABCDE, moeAB, nac, napFDAGHBC-ccmABCDEFGH, narGHJI, narKS, narXL, ndh, nfeR, nikABCDER,
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First gene in the operon(s) aceE, ackA, acnA, acrE, adhE, aer, aldA, ansB, arcA, aspA, aspC, bcsB, cadC, caiF, caiT, citC, cydA, cydD, cyoA, dcuB, dcuC, dcuS, dmsA, dpiB, dppA, emrK, fdhF, fdnG, feoA, fes, fixA, fnr, fnrS, focA, frdA, fumA, fumB, fumC, gadA, gadX, garP, gcvT, gdhA, glnD, glnK, glpA, glpT, gltB, gnd, grcA, hcp, hemA, hlyE, hmp, hyfA, hypB, idlP, iraM, katG, lpd, malP, moaA, moeA, nac, napF,
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Simple and complex regulons AcrR,FNR,Fur,SoxR
AcrR,FNR,Fur,SoxR,SoxS
AdiY,ArcA,CRP,FNR,Fis,GadE-RcsB,GadW,GadX,H-NS,RcsB,TorR
AdiY,ArcA,CRP,FNR,Fis,GadE-RcsB,GadW,GadX,H-NS,RcsB,TorR,ppGpp
AdiY,ArgR,CRP,FNR,Fur,GadE,HdfR,IHF,Lrp,Nac
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Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[FNR,-](59)
[FNR,+](79)


Transcription factor regulation    


Transcription factor binding sites (TFBSs) arrangements
      

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence LeftPos RightPos Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
  FNR repressor aceEp1 Sigma70 nd nd aceE, aceF
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [1], [2]
  FNR repressor aceEp2 Sigma38 nd nd aceE, aceF
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [1], [2]
  FNR activator ackAp Sigma32 nd nd ackA
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [2]
  FNR repressor acnAp2 Sigma70 -40.5 -90.5 acnA
tttatcaattTGGGTTGTTATCAAatcgttacgc
 1335734 1335747 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [3]
  FNR activator acrEp Sigma70 nd nd acrE, acrF
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [4], [4]
  FNR activator adhEp2 Sigma38 -42.5 -230.5 adhE
ttgcaaaaatTTGATTTGGATCACgtaatcagta
 1298345 1298358 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ] S [5], [6]
  FNR activator aerp Sigma28 -49.5 -93.5 aer
atcgcaaattGCGATCTAAATCAAattaatcggt
 3219163 3219176 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ] S [6], [7], [7]
  FNR repressor aldAp Sigma70 -10.5 -52.5 aldA
tctctgatgaTTGATGTTAATTAAcaatgtattc
 1488173 1488186 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7], [7]
  FNR activator ansBp2 Sigma70 -41.5 -64.5 ansB
acgttgtaaaTTGTTTAACGTCAAatttcccata
 3100786 3100799 [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] S [8]
  FNR activator arcAp1 Sigma70 -82.5 -284.5 arcA
acaattgaacTTGATATATGTCAAcgaagcgtag
 4640584 4640597 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ] S [6], [9], [9], [10]
  FNR repressor arcAp3 Sigma70 -55.5 -284.5 arcA
acaattgaacTTGATATATGTCAAcgaagcgtag
 4640584 4640597 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ] S [6], [9], [9], [10]
  FNR activator aspAp Sigma70 -40.5 -145.5 aspA, dcuA
gacacttaaaGTGATCCAGATTACggtagaaatc
 4368466 4368479 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ] S [6], [11], [11], [12]
  FNR activator aspCp nd nd nd aspC
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [10]
  FNR repressor aspCp nd nd nd aspC
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [10]
  FNR activator bcsBp Sigma70 nd nd bcsB, bcsZ
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [4], [4]
  FNR activator cadCp Sigma70 -156.5 -185.5 cadC
atgatgaattTTGATGGTAAGGAAtattacttct
 4362113 4362126 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7], [7]
  FNR activator caiFp Sigma70 -55.5 -137.5 caiF
atcgatatttTTGATGACATAAGCaggatttagc
 34156 34169 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] S [6], [13]
  FNR activator caiTp Sigma70 -90.5 -196.5 caiT, caiA, caiB, caiC, caiD, caiE
aaactgattaTTAATCAAAATTAAcgaaaaaacg
 42121 42134 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [4], [4], [7], [7]
  FNR activator caiTp Sigma70 -41.5 -147.5 caiT, caiA, caiB, caiC, caiD, caiE
aaacaaaaatGTGATACCAATCACagaatacagc
 42072 42085 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [4], [4], [7], [7]
  FNR repressor citCp2 nd 11.5 -172.5 citC, citD, citE, citF, citX, citG
ctaactctatGTGAAATAAATCAAaatttcacgc
 652022 652035 [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [14], [14]
  FNR repressor cydAp1 Sigma70 -53.5 -341.5 cydA, cydB
tttgtaggaaTTGATATTTATCAAtgtataagtc
 771110 771123 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [4], [6], [15], [16], [17], [18], [18], [19], [19], [20]
  FNR repressor cydAp1 Sigma70 -1.5 -289.5 cydA, cydB
aagagataaaTTGTTCTCGATCAAattggctgaa
 771162 771175 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [4], [6], [15], [16], [18], [18], [19], [19], [20], [21]
  FNR activator cydAp2 Sigma70 -167.5 -341.5 cydA, cydB
tttgtaggaaTTGATATTTATCAAtgtataagtc
 771110 771123 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [4], [6], [18], [18], [19], [19], [20]
  FNR repressor cydAp2 Sigma70 -115.5 -289.5 cydA, cydB
aagagataaaTTGTTCTCGATCAAattggctgaa
 771162 771175 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [4], [6], [18], [18], [19], [20], [21]
  FNR repressor cydAp3 Sigma70 -85.5 -341.5 cydA, cydB
tttgtaggaaTTGATATTTATCAAtgtataagtc
 771110 771123 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [4], [6], [18], [18], [19], [19], [20]
  FNR repressor cydAp3 Sigma70 -33.5 -289.5 cydA, cydB
aagagataaaTTGTTCTCGATCAAattggctgaa
 771162 771175 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [4], [6], [18], [18], [19], [20], [21]
  FNR repressor cydAp4 Sigma70 -96.5 -341.5 cydA, cydB
tttgtaggaaTTGATATTTATCAAtgtataagtc
 771110 771123 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [4], [6], [18], [18], [19], [19], [20]
  FNR repressor cydAp4 Sigma70 -44.5 -289.5 cydA, cydB
aagagataaaTTGTTCTCGATCAAattggctgaa
 771162 771175 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [4], [6], [18], [18], [19], [20], [21]
  FNR activator cydDp Sigma70 -90.5 -159.5 cydD, cydC
atggcagcacTTGATGCGGAACGCtacctcgatg
 931115 931128 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [22]
  FNR repressor cyoAp Sigma70 -192.5 -235.5 cyoA, cyoB, cyoC, cyoD, cyoE
ttgttaaataATTGTTTTATTTCAcattggttat
 451839 451852 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [4], [7], [7], [10], [11], [15]
  FNR activator dcuBp1 Sigma70 -45.5 -65.5 dcuB, fumB
ctgaaaacagTTCATACAAAACAGaacgtgactg
 4348803 4348816 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [12], [23]
  FNR activator dcuCp nd -115.5 -230.5 dcuC
gctaacaccaTTGCAATTAACAAAtttgcatcaa
 656192 656205 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ] S [6], [24]
  FNR activator dcuCp nd -63.5 -178.5 dcuC
acattattatGTGATAATTGCCAAccgctaaata
 656140 656153 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ] S [6], [24]
  FNR activator dcuCp nd -33.5 -148.5 dcuC
aatatgcgttTTGTTATCTATGTAtaaaaacagc
 656110 656123 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ] S [6], [24], [24]
  FNR activator dcuSp Sigma70 nd nd dcuS, dcuR
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [4], [4]
  FNR activator dmsAp1 Sigma70 -41.5 -177.5 dmsA, dmsB, dmsC
ttgtctccctTTGATACCGAACAAtaattactcc
 940775 940788 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [25], [25], [26], [26], [27], [27], [28]
  FNR repressor dpiBp1 nd 45.5 -206.5 dpiB, dpiA
gcgtgaaattTTGATTTATTTCACatagagttag
 652022 652035 [COMP-AINF-SIMILAR-TO-CONSENSUS] W [14], [14]
  FNR repressor dppAp Sigma70 -162.5 -327.5 dppA, dppB, dppC, dppD, dppF
tcaccaaatgTTGCTAAATATTAAgctgattgtt
 3708026 3708039 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7], [7]
  FNR activator emrKp nd nd nd emrK, emrY
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [4], [4]
  FNR activator fdhFp Sigma54 nd nd fdhF
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [4]
  FNR activator fdnGp Sigma70 -97.5 -126.5 fdnG, fdnH, fdnI
tctaccgctaTTGAGGTAGGTCAAtttgcgaagg
 1547268 1547281 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IMP-SITE-MUTATION] C [6], [29], [29]
  FNR repressor fdnGp Sigma70 -97.5 -126.5 fdnG, fdnH, fdnI
tctaccgctaTTGAGGTAGGTCAAtttgcgaagg
 1547268 1547281 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IMP-SITE-MUTATION] C [6], [29], [29]
  FNR activator fdnGp Sigma70 -42.5 -71.5 fdnG, fdnH, fdnI
gatgttctttTTGATTTCGCGCAAaaagattcag
 1547323 1547336 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IMP-SITE-MUTATION] C [6], [11], [29], [29]
  FNR activator feoAp Sigma70 -90.5 -196.5 feoA, feoB, feoC
gctgcgatatAACCTTGAGCCACATCAACATTGagtcagatta
 3539956 3539978 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ] S [6], [30], [30]
  FNR activator fesp Sigma70 -143.5 -193.5 fes, ybdZ, entF, fepE
aactgtcgggCATGGTCGTCATCAacacgacgca
 612537 612550 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ] S [6], [7], [7]
  FNR activator fixAp Sigma70 -197.5 -275.5 fixA, fixB, fixC, fixX
cgttttttcgTTAATTTTGATTAAtaatcagttt
 42121 42134 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [4], [4], [7], [7]
  FNR activator fnrSp Sigma70 -42.5 -42.5 fnrS
gccgcaaagtTTGAGCGAAGTCAAtaaactctct
 1409080 1409093 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [6], [31], [31]
  FNR repressor fnrp Sigma70 -0.5 -26.5 fnr
gatgttaaaaTTGACAAATATCAAttacggcttg
 1399546 1399559 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [6], [32], [32], [33]
  FNR activator focAp1 Sigma70 -40.5 -67.5 focA, pflB
caggcgagatATGATCTATATCAAtttctcatct
 954527 954540 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] C [6], [34], [34], [35], [36], [37], [38], [39], [40]
  FNR activator focAp3 Sigma70 -58.5 -406.5 focA, pflB
gcattctgggCAAAATAAAATCAAatagcctacg
 954866 954879 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] S [2], [34], [34], [36], [37], [38], [39], [40]
  FNR activator frdAp Sigma70 -45.5 -139.5 frdA, frdB, frdC, frdD
actaaaaaaaTCGATCTCGTCAAAtttcagactt
 4382451 4382464 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] S [2], [6], [23], [28], [41]
  FNR activator frdAp2 Sigma38 -45.5 -139.5 frdA, frdB, frdC, frdD
actaaaaaaaTCGATCTCGTCAAAtttcagactt
 4382451 4382464 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] S [2], [6], [23], [28], [41]
  FNR repressor fumAp Sigma70 nd nd fumA, fumC
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [42]
  FNR activator fumBp Sigma70 -114.5 -136.5 fumB
tctgccggggTTGATTGGTGTGAGcgtatcgtgc
 4347456 4347469 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] W [11], [11], [43], [43], [44]
  FNR activator fumBp Sigma70 -61.5 -83.5 fumB
ccgcgatgtaCGGGTTCTTATAAAtgcactttgc
 4347403 4347416 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] W [43], [43], [44]
  FNR activator fumBp Sigma70 -57.5 -79.5 fumB
gatgtacgggTTCTTATAAATGCActttgcgtgc
 4347399 4347412 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] W [43], [43], [44]
  FNR repressor fumCp2 Sigma38 nd nd fumC
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [10]
  FNR repressor gadAp Sigma70 11.5 -16.5 gadA, gadX
ttattgccttCAAATAAATTTAAGgagttcgaaa
 3667590 3667603 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7], [7]
  FNR repressor gadAp2 Sigma38 11.5 -16.5 gadA, gadX
ttattgccttCAAATAAATTTAAGgagttcgaaa
 3667590 3667603 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7], [7]
  FNR repressor gadXp Sigma38 -159.5 -188.5 gadX, gadW
aagggattatTTGCTTACTATTAAtttccctgtg
 3665992 3666005 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7], [7]
  FNR activator garPp Sigma70 nd nd garP, garL, garR, garK, rnpB
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7], [7]
  FNR activator gcvTp Sigma70 nd nd gcvT, gcvH, gcvP
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [4], [4]
  FNR activator gdhAp Sigma70 nd nd gdhA
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [10]
  FNR activator glnDp nd nd nd glnD
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [10]
  FNR repressor glnDp nd nd nd glnD
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [10]
  FNR activator glnKp Sigma54 nd nd glnK, amtB
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [10]
  FNR repressor glnKp Sigma54 nd nd glnK, amtB
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [10]
  FNR activator glpABCp Sigma70 -40.5 -104.5 glpA, glpB, glpC
gttcaaaatgACGCATGAAATCACgtttcacttt
 2352536 2352549 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [45], [46], [46], [47], [48]
  FNR activator glpABCp Sigma70 -0.5 -64.5 glpA, glpB, glpC
atgagcgaatATGCGCGAAATCAAacaattcatg
 2352576 2352589 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [45], [46], [46], [47], [48]
  FNR activator glpTQp Sigma70 -131.5 -208.5 glpT, glpQ
catgaattgtTTGATTTCGCGCATattcgctcat
 2352576 2352589 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [46], [46], [47], [47], [48]
  FNR activator glpTQp Sigma70 -91.5 -168.5 glpT, glpQ
aaagtgaaacGTGATTTCATGCGTcattttgaac
 2352536 2352549 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [46], [46], [47], [47], [48]
  FNR repressor gltBp Sigma70 -26.5 -242.5 gltB, gltD, gltF
agcttgccatTTGACCTGTATCAGctttcccgat
 3354476 3354489 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ] S [6], [7], [7], [10]
  FNR repressor gltBp2 Sigma38 -26.5 -242.5 gltB, gltD, gltF
agcttgccatTTGACCTGTATCAGctttcccgat
 3354476 3354489 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ] S [6], [7], [7], [10]
  FNR repressor gndp Sigma70 nd nd gnd
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [10]
  FNR repressor grcAp1 Sigma70 -93.5 -167.5 grcA
cccgcataagTTGATGTAAAACAAtaaaatccat
 2716610 2716623 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [10], [49], [50], [51]
  FNR activator grcAp1 Sigma70 -40.5 -114.5 grcA
gtggtttttaTTGATTTAAATCAAagattcaagg
 2716557 2716570 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [2], [6], [49], [50], [51]
  FNR repressor grcAp1 Sigma70 -40.5 -114.5 grcA
gtggtttttaTTGATTTAAATCAAagattcaagg
 2716557 2716570 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [2], [6], [49], [50], [51]
  FNR activator hcpp1 nd -72.5 -103.5 hcp, hcr, poxB
gccgccaaaaTTGCGCTAAATCAAtctcccttaa
 913911 913924 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [52], [52], [53], [53], [54]
  FNR repressor hemAp1 Sigma70 -24.5 -62.5 hemA, prfA, prmC
ctctcttttaTTGATCTTACGCATcctgtatgat
 1263645 1263658 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [6], [27], [55], [55], [56], [56]
  FNR activator hlyEp nd -61.5 -133.5 hlyE
taaacattgtTTGATATTTATCATattaatagaa
 1230521 1230534 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [57], [57], [58]
  FNR repressor hmpp Sigma38 5.5 -33.5 hmp
taagatgcatTTGAGATACATCAAttaagatgca
 2685795 2685808 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [59], [59], [60], [61]
  FNR repressor hyfAp Sigma54 -105.5 -135.5 hyfA, hyfB, hyfC, hyfD, hyfE, hyfF, hyfG, hyfH, hyfI, hyfJ, hyfR, focB
aatccattttTTGCTGAACGTTAAtgaccatcat
 2601059 2601072 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [62], [62]
  FNR activator hypBp nd -149.5 -311.5 hypB, hypC, hypD, hypE, fhlA
ggcactggaaTTGATCGAACAGCAggccgcaaaa
 2850683 2850696 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [6], [63], [63]
  FNR activator hypBp nd -43.5 -205.5 hypB, hypC, hypD, hypE, fhlA
gccttttgttTTGATCTGGTTTGCcgcggcagcg
 2850789 2850802 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [63], [63]
  FNR activator idlPp Sigma38 nd nd idlP, iraD
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7], [7]
  FNR activator iraDp2 Sigma70 nd nd idlP, iraD
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7], [7]
  FNR activator iraMp1 nd -70.5 -157.5 iraM
aaatctcattTTGTTTAACATCCAttgagattcc
 1212154 1212167 [COMP-AINF-SIMILAR-TO-CONSENSUS] W [64], [64]
  FNR activator katGp Sigma70 -112.5 -135.5 katG
atcaaaaaagCTTAATTAAGATCAatttgatcta
 4133693 4133706 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ] S [6], [7], [7]
  FNR activator katGp Sigma70 -96.5 -119.5 katG
taagatcaatTTGATCTACATCTCtttaaccaac
 4133709 4133722 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-CHIP], [EXP-CHIP-SEQ] S [6], [7], [7], [65], [65]
  FNR activator lpdAp Sigma70 nd nd lpd
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [4], [4], [10]
  FNR repressor lpdAp Sigma70 nd nd lpd
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [4], [4], [10]
  FNR activator malPp Sigma70 -127.5 -164.5 malP, malQ
ttgcattgatTTGATGCTAATCCTgtggtttgca
 3552631 3552644 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7], [7]
  FNR activator moaAp1 nd -39.5 -256.5 moaA, moaB, moaC, moaD, moaE
tgcctccctgATGATGTATATCAAagtaaaaccg
 816781 816794 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ] S [6], [66], [66], [67]
  FNR repressor moeAp Sigma70 34.5 4.5 moeA, moeB
caggagtgttTTCATGGAATTTACcaccggattg
 866354 866367 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [68], [68]
  FNR repressor nacp Sigma54 nd nd nac
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [10]
  FNR activator napFp1 Sigma70 -64.5 -141.5 napF, napD, napA, napG, napH, napB, napC, ccmA, ccmB, ccmC, ccmD, ccmE, ccmF, ccmG, ccmH
cgccactcttTTGATCCTGCTACAggttttaccc
 2303632 2303645 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IMP-SITE-MUTATION] C [6], [69], [69], [70], [70]
  FNR activator narGp Sigma70 -41.5 -98.5 narG, narH, narJ, narI
cccatcactcTTGATCGTTATCAAttcccacgct
 1279759 1279772 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [26], [27], [27], [33], [71]
  FNR activator narKp1 Sigma70 -79.5 -104.5 narK, narS
actatgggtaATGATAAATATCAAtgatagataa
 1277846 1277859 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] C [6], [72]
  FNR activator narKp1 Sigma70 -41.5 -66.5 narK, narS
atcttatcgtTTGATTTACATCAAattgccttta
 1277884 1277897 [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [27], [27], [65], [65], [73]
  FNR repressor narXp Sigma70 -106.5 -265.5 narX, narL
aatttgatgtAAATCAAACGATAAgataacttta
 1277877 1277890 [COMP-AINF-PATTERN-DISCOVERY], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-CHIP], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] W [6], [65], [74], [75]
  FNR repressor narXp Sigma70 -75.0 -234.0 narX, narL
tatctatcatTGATATTTATCATTacccatagtg
 1277845 1277858 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [6], [75]
  FNR repressor narXp Sigma70 107.5 -52.5 narX, narL
ccattccagaATGTATCGTCACATtcattaaggt
 1277664 1277677 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] W [75]
  FNR repressor ndhp Sigma70 -94.5 -187.5 ndh
actctgttttTTGATCTCACCCGGtaaagtcgcc
 1165891 1165904 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] C [4], [6], [10], [76], [76], [77]
  FNR repressor ndhp Sigma70 -50.5 -143.5 ndh
gcaacaaaacTTGATTAACATCAAttttggtatg
 1165935 1165948 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] C [4], [6], [10], [76], [76], [77]
  FNR activator nfeRp nd nd nd nfeR
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7], [7]
  FNR activator nikAp1 nd -40.5 -79.5 nikA, nikB, nikC, nikD, nikE, nikR
tgcccatctaTTGATCCAGAACAGGtaatcagtat
 3613581 3613595 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IMP-SITE-MUTATION] C [6], [78], [79]
  FNR activator nirBp Sigma70 -41.5 -65.5 nirB, nirD, nirC, cysG
aaaggtgaatTTGATTTACATCAAtaagcggggt
 3493939 3493952 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [28], [28], [33], [33], [80], [80], [81], [81], [82], [82]
  FNR repressor norVp Sigma54 -140.5 -177.5 norV, norW
aaactcatctTTGCCTCACTGTCAatttgactat
 2832292 2832305 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [83], [83]
  FNR activator nrdDp Sigma70 -64.5 -242.5 nrdD, nrdG
gctttttactTTGAGCTACATCAAaaaaagctca
 4462896 4462909 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [84], [84], [85], [85]
  FNR activator nrdDp Sigma70 -33.5 -211.5 nrdD, nrdG
tcaaacatccTTGATGCAAAGCACtatatataga
 4462865 4462878 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [84], [84], [85], [85]
  FNR activator nrfAp Sigma70 -41.5 -134.5 nrfA, nrfB, nrfC, nrfD, nrfE, nrfF, nrfG
gcacttacaaTTGATTAAAGACAAcattcacagt
 4287623 4287636 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [6], [86], [86], [87], [87]
  FNR repressor nuoAp2 Sigma70 -40.5 -130.5 nuoA, nuoB, nuoC, nuoE, nuoF, nuoG, nuoH, nuoI, nuoJ, nuoK, nuoL, nuoM, nuoN
gaaaggagtaAAAAACCACATCAAttagctgtat
 2405196 2405209 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] S [4], [10], [88]
  FNR repressor ompWp nd -126.5 -155.5 ompW
tatttaaaaaTTGATTTAAATCACattaaccagg
 1313858 1313871 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [6], [89], [89]
  FNR activator ompWp nd -81.5 -110.5 ompW
aacttctaaaTTAATCCAGATCAAtaaagggtga
 1313903 1313916 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [6], [7], [7], [89], [89]
  FNR repressor ompXp2 nd nd nd ompX
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7], [7]
  FNR activator pdhRp Sigma70 -50.5 -108.5 pdhR, aceE, aceF, lpd
gcacagtttcATGATTTCAATCAAaacctgtatg
 121977 121990 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] S [1], [1], [4], [6], [7]
  FNR repressor pdhRp Sigma70 -50.5 -108.5 pdhR, aceE, aceF, lpd
gcacagtttcATGATTTCAATCAAaacctgtatg
 121977 121990 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] S [1], [1], [4], [6], [7]
  FNR activator pdhRp2 Sigma38 -50.5 -108.5 pdhR, aceE, aceF, lpd
gcacagtttcATGATTTCAATCAAaacctgtatg
 121977 121990 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] S [1], [1], [4], [6], [7]
  FNR repressor pdhRp2 Sigma38 -50.5 -108.5 pdhR, aceE, aceF, lpd
gcacagtttcATGATTTCAATCAAaacctgtatg
 121977 121990 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] S [1], [1], [4], [6], [7]
  FNR activator pepTp nd nd nd pepT
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7], [7]
  FNR activator pitAp nd nd nd pitA
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7], [7]
  FNR activator pstSp Sigma70 nd nd pstS, pstC, pstA, pstB, phoU
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [4], [4]
  FNR activator pstSp2 Sigma38 nd nd pstS, pstC, pstA, pstB, phoU
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [4], [4]
  FNR repressor purMp Sigma70 -192.5 -236.5 purM, purN
attcttttcgTTGACTTTAGTCAAaatgataacg
 2620954 2620967 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IMP-SITE-MUTATION] C [4], [4], [6], [90], [90]
  FNR repressor puuAp Sigma38 29.0 -32.0 puuA, ymjE, puuP
attttacgctTTGATAACGAGCGGaaaacaaacc
 1360933 1360946 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [64], [64]
  FNR activator ravAp Sigma38 -201.5 -236.5 ravA, viaA
cgggcaatgaTTGCTTATTATCAGtgctcataga
 3931323 3931336 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [91], [91]
  FNR activator ravAp Sigma38 -71.5 -106.5 ravA, viaA
tgcggccacaTTAACCTGGCTCAAagaaaaatac
 3931193 3931206 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [91], [91]
  FNR repressor rplMp nd nd nd rplM, rpsI
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [4], [4]
  FNR repressor rplTp nd nd nd rplT, pheM
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [4]
  FNR activator rpsJp Sigma70 nd nd rpsJ, rplC, rplD, rplW, rplB, rpsS, rplV, rpsC, rplP, rpmC, rpsQ
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [4]
  FNR repressor rpsPp Sigma70 nd nd rpsP, rimM, trmD, rplS
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [4]
  FNR repressor sdhCp Sigma70 nd nd sdhC, sdhD, sdhA, sdhB, sucA, sucB, sucC, sucD, sdhX
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [10], [92], [92]
  FNR repressor sodAp Sigma70 -37.5 -88.5 sodA
aagtacggcaTTGATAATCATTTTcaatatcatt
 4100715 4100728 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] W [10], [93], [94]
  FNR repressor soxRp Sigma70 nd nd soxR
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [10]
  FNR repressor soxSp Sigma70 nd nd soxS
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [10]
  FNR activator ssuEp Sigma70 nd nd ssuE, ssuA, ssuD, ssuC, ssuB
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [4], [4]
  FNR repressor sucAp Sigma38 nd nd sucA, sucB, sucC, sucD, sdhX
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [95], [96]
  FNR activator tarp Sigma28 nd nd tar, tap, cheR, cheB, cheY, cheZ
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7], [7]
  FNR activator tdcAp nd -148.5 -176.5 tdcA, tdcB, tdcC, tdcD, tdcE, tdcF, tdcG
gtcattttttTTGACAAAAATCAGggtttatgct
 3267235 3267248 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7], [7]
  FNR activator tdcAp nd -105.5 -133.5 tdcA, tdcB, tdcC, tdcD, tdcE, tdcF, tdcG
actttaacttGTTGATATTTAAAGgtatttaatt
 3267192 3267205 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7], [7]
  FNR repressor tpxp Sigma70 -18.5 -51.5 tpx
tgctgtgttaTTGACAGTTAGCATaaactaggtg
 1388856 1388869 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [97]
  FNR repressor ubiCp Sigma70 -0.5 -63.5 ubiC, ubiA
atcacttaatTTGCTTTACATCTCccgtaaacac
 4252436 4252449 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [98], [98]
  FNR activator uppp Sigma70 -61.5 -98.5 upp, uraA
tatctcaaacCGTTATCATTTTGActaaagtcaa
 2620964 2620977 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ] S [6], [7], [7]
  FNR activator uxaCp2 Sigma70 nd nd uxaC, uxaA
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7], [7]
  FNR activator xdhAp1 nd nd nd xdhA, xdhB, xdhC
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [4], [4]
  FNR activator ybdNp Sigma70 -303.5 -420.5 ybdN
tcagcaggggTTGATGATATTCAAatggaaatag
 636983 636996 [COMP-AINF-SIMILAR-TO-CONSENSUS] W [64], [64]
  FNR activator ybdNp Sigma70 -26.5 -143.5 ybdN
atgagagtttTTGATATATAACTAcagacagcta
 636706 636719 [COMP-AINF-SIMILAR-TO-CONSENSUS] W [64], [64]
  FNR repressor ychOp Sigma70 nd nd ychO
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7], [7]
  FNR activator ydeJp Sigma70 -404.5 -489.5 ydeJ
gtcctctcctTTGTGAGAAATCAAattaccgcgt
 1624277 1624290 [COMP-AINF-SIMILAR-TO-CONSENSUS] W [64], [64]
  FNR activator ydhYp Sigma38 -42.5 -207.5 ydhY, ydhV, ydhW, ydhX, ydhU, ydhT
gtaattttaaTTGATAACGATCAAtgttaagggc
 1754678 1754691 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [99], [100], [100]
  FNR activator yecRp nd nd nd yecR
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7], [7]
  FNR repressor yeiLp Sigma38 -28.5 -93.5 yeiL
gggccgatgaTTGAATCTTAACAAcagcgtacgt
 2255255 2255268 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [101]
  FNR activator yfgFp nd -41.5 -134.5 pdeF
gttattttgtTTGATATATATCAAttggtacttt
 2629066 2629079 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [6], [102], [102]
  FNR repressor ygbAp nd nd nd ygbA
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7], [7]
  FNR activator yhjAp Sigma70 -41.5 -114.5 ccp
atgtaattgaTTGATTCCTATCAAaaagcgtatc
 3669296 3669309 [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [103], [103]
  FNR activator ynfEp Sigma70 -40.5 -106.5 ynfE, ynfF, ynfG, ynfH, dmsD
tacccttctaTTGATATGGATTAATaattcttaac
 1657956 1657970 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [7], [7], [99], [99], [104], [104]
  FNR activator ynfEp2 Sigma38 -40.5 -106.5 ynfE, ynfF, ynfG, ynfH, dmsD
tacccttctaTTGATATGGATTAATaattcttaac
 1657956 1657970 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [7], [7], [99], [99], [104], [104]
  FNR repressor ysgAp Sigma70 nd nd ysgA
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7], [7]
  FNR repressor ytfEp nd nd nd ytfE
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [105]
  FNR repressor zwfp Sigma70 nd nd zwf
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [10]



High-throughput Transcription factor binding sites (TFBSs)
      

  Functional conformation Function Object name Object type Distance to first Gene Sequence LeftPos RightPos Center Position Growth Condition Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
  FNR activator narG Gene nd
aattatatagAGTAAAATATTTGATTatcctttgcg
1279472 1279487 1279479.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP] S [65]
  FNR activator arcA Gene nd
aattgtagcaCGTTAACAGTTTGATGaaatcatcgt
4640612 4640627 4640619.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP], [EXP-CHIP-SEQ] S [65]
  FNR activator aroP Gene nd
ggatttttatAGTTTAATAATCGTTAaaaaactcct
121869 121884 121876.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP] S [65]
  FNR activator aroP Gene nd
atttgtgcatAGTTACAACTTTGAAAcgttatatat
121923 121938 121930.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP], [EXP-CHIP-SEQ] S [65]
  FNR activator yffS Gene nd
attgcgaataGCAACAACTAAACAACcaatacaccc
2564382 2564397 2564389.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP], [EXP-CHIP-SEQ] S [65]
  FNR activator focA Gene nd
taaccttataATTACAATTATTTTATtaatgcaaat
954762 954777 954769.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP] S [65]
  FNR activator fnr Gene nd
aaatatatgtCTATCTATTTGAAAACccttaagttg
1399641 1399656 1399648.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP], [EXP-CHIP-SEQ] S [65]
  FNR activator adhE Gene nd
tatagctaacAGTTAATAAATTGTAGtatgatttgg
1298411 1298426 1298418.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP], [EXP-CHIP-SEQ] S [65]
  FNR activator metV Gene nd
ccgtgatcggGGTAAAAAAAAGGTTGcatgaaaacg
2947333 2947348 2947340.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP], [EXP-CHIP-SEQ] S [65]
  FNR activator mltA Gene nd
ccgtgatcggGGTAAAAAAAAGGTTGcatgaaaacg
2947333 2947348 2947340.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP], [EXP-CHIP-SEQ] S [65]
  FNR activator ydfO Gene nd
ctgcatcaacTTAACGTAAAAACAACttcagacaat
1636697 1636712 1636704.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP], [EXP-CHIP-SEQ] S [65]
  FNR activator bidA Gene nd
tggtagaacaGTTAAAAAATGTTAACcctgcaacag
1667333 1667348 1667340.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP], [EXP-CHIP-SEQ] S [65]
  FNR activator aroP Gene nd
tccgtttgttGTATTAATTTGTTTACatcaaagaag
121623 121638 121630.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP] S [65]
  FNR activator yfcZ Gene nd
atcatagtctTAACCATTTTTTTACAtttagccaag
2460521 2460536 2460528.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP] S [65]
  FNR activator aroP Gene nd
atggacataaGGTGAATACTTTGTTActttagcgtc
122008 122023 122015.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP], [EXP-CHIP-SEQ] S [65]
  FNR activator focA Gene nd
atcctccgctAAAACAGTTAATTAAAagggagcatc
954671 954686 954678.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP] S [65]
  FNR activator arcA Gene nd
ctagttgcatCATACAACTAATAAACgtggtgaatc
4640689 4640704 4640696.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP] S [65]
  FNR activator thrA Gene nd
gccgtgagtaAATTAAAATTTTATTGacttaggtca
98 113 105.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP], [EXP-CHIP-SEQ] S [65]
  FNR activator ung Gene nd
gcggccaattGGTAAAACCATTGTTGcttgagtgta
2716503 2716518 2716510.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP], [EXP-CHIP-SEQ] S [65]
  FNR activator fdnG Gene nd
gctgaattttATAGCATTTTTTTAACtggcctgtca
1547216 1547231 1547223.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP], [EXP-CHIP-SEQ] S [65]
  FNR activator katG Gene nd
ggttcgacctGGTTTATAAATAGTGTggcttttgtg
4133498 4133513 4133505.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP] S [65]
  FNR activator ortT Gene nd
gtcattgcccATATGAACGAATTATTaatcgccctg
1517712 1517727 1517719.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP] S [65]
  FNR activator yffS Gene nd
gttgttgctgATAACATCCTGGTAAAataccatttc
2564236 2564251 2564243.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP] S [65]
  FNR activator focA Gene nd
ttaccgatatTTAACCTTATAATTACaattatttta
954751 954766 954758.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP] S [65]
  FNR activator narK Gene nd
taaagttatcTTATCGTTTGATTTacatcaaatt
1277877 1277890 1277883.5 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-CHIP], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] S [65]
  FNR activator focA Gene nd
ttaaatacaaATTACCGATATTTAACcttataatta
954740 954755 954747.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP] S [65]
  FNR activator grcA Gene nd
gcggccaattGGTAAAACCATTGTTGcttgagtgta
2716503 2716518 2716510.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP], [EXP-CHIP-SEQ] S [65]
  FNR activator katG Gene nd
tcacacagtgATCACAAATTTTAAACagagcacaaa
4133538 4133553 4133545.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP] S [65]
  FNR activator bidA Gene nd
ctggcccaaaTTGAGATAGCGCAAattttggtag
1667305 1667318 1667311.5 nd [EXP-IEP-MICROARRAY], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [106]
  FNR activator garD Gene nd
tgagaccaggTCCTCATTTTAATAACccctggctgg
3275243 3275258 3275250.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP], [EXP-CHIP-SEQ] S [65]
  FNR activator pykA Gene nd
tggttgtttcAGTCAACGGAGTATTAcatgtccaga
1937632 1937647 1937639.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP] S [65]
  FNR activator focA Gene nd
gcaaatacggAGTAAATATTTGATTAtccaaataaa
954593 954608 954600.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP], [EXP-CHIP-SEQ] S [65]
  FNR activator yibN Gene nd
ttgagtatgaGGTTGTCGCAATGTTGgtttctaaaa
3785250 3785265 3785257.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP], [EXP-CHIP-SEQ] S [65]
  FNR activator scpA-argK-scpBC Transcription-Unit nd
nd
nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [4]
  FNR activator ydfZ Transcription-Unit nd
nd
nd nd nd nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [107]
  FNR repressor msrB Gene nd
taagttgctgAATCGTTTTTTCAACCgttgatttct
1862006 1862021 1862013.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP] S [65]
  FNR repressor cydA Gene nd
agccttataaCTCACACATTTTAAACataaatgtca
771040 771055 771047.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP] S [65]
  FNR repressor msrB Gene nd
aattttacagGCAACCTTTTATTCACtaacaaatag
1862733 1862748 1862740.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP], [EXP-CHIP-SEQ] S [65]
  FNR repressor cydA Gene nd
gattttgcggCGTAATATATACGTGGgatcaatttg
771272 771287 771279.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP], [EXP-CHIP-SEQ] S [65]
  FNR repressor msrB Gene nd
gtgactgattCTAACAAAACATTAACaccaactggc
1862475 1862490 1862482.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP] S [65]
  FNR repressor cydA Gene nd
tcacacatttTAAACATAAATGTCACtaaagttacc
771051 771066 771058.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP] S [65]
  FNR repressor cydA Gene nd
tgagtttttaTTAACATGTTTGCAACctttctttac
771306 771321 771313.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP] S [65]
  FNR repressor cydA Gene nd
tgtcactaaaGTTACCTTATTGAAACatgattaaca
771071 771086 771078.0 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-CHIP] S [65]
  FNR repressor gapC_1C_2 Transcription-Unit nd
nd
nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [4]
  FNR repressor ycaC Transcription-Unit nd
nd
nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [7]
Other High-throughput regulatory interactions with weak evidence


Alignment and PSSM for FNR TFBSs    

Aligned TFBS of FNR   
  Sequence
  TTGATGTAAATCAA
  TTGATGTTAATCAA
  TTGATTTAAATCAA
  TTGATATTTATCAA
  TTGATATATATCAA
  TTGATGTAGCTCAA
  TTGATATAGATCAT
  TTGATTTAAATCAC
  TTGATGTGGCTCAA
  TTGATAACGATCAA
  TTGATAACGATCAA
  TTGATGTAAAACAA
  TTGATTTGGATCAC
  TTGATGTATCTCAA
  TTGATAGGAATCAA
  TTGACATATATCAA
  TTGATATTTATCAT
  TTGATATTTATCAT
  TTGATTTAGCGCAA
  TTGATGTTAATTAA
  TTGATTTCGCGCAA
  TTGATCTTAATTAA
  TTGATATGGATTAA
  TTGACTTCGCTCAA
  TTGACGTTAAACAA
  TTGTTCTCGATCAA
  TTGATGATATTCAA
  TTGATCTGGATTAA
  TTGATTGAAATCAT
  TTGATATACATCAT
  TTGATTTAGATCGC
  TTGATGCAAAGCAC
  TTGACAAATATCAA
  TTGATCTTACGCAT
  TTGATACCGAACAA
  TTGATTTCGCGCAT
  TTGATTTATTTCAC
  TTGTCTTTAATCAA
  TTGATTTCTCACAA
  TTGACAAAAATCAG
  TTGATGGTAAGGAA
  TTGACCTGTATCAG
  TTAATATTTAGCAA
  TTGACCTACCTCAA
  TTGATATATAACTA
  TTGACTTTAGTCAA
  TTGATGACGACCAT
  TTGATGCTAATCCT
  TTAATAGTAAGCAA
  TTGATCCAGAACAG
  TTAATTTTGATTAA
  GTGATACCAATCAC
  TTGATCTACATCTC
  TTAACCTGGCTCAA
  TTGACAGTTAGCAT
  TTGATAACGAGCGG
  TTGTTAAGATTCAA
  TTGTTTTATTTCAC
  TTGATAACAACCCA
  TGGATGTTAAACAA
  TTGATGCGGAACGC
  TTAACGTTCAGCAA
  CTGATAATAAGCAA
  GTAATCTGGATCAC
  TTGATCTGGTTTGC
  TTGATCTCACCCGG
  GAGATGTAAAGCAA
  TTGTTGATATTTAA
  TTGTTATCTATGTA
  TTGACAGTGAGGCA
  TTGATGTGGTTTTT
  TTGATTTTATTTTG
  TTGGCAATTATCAC
  GTGATTTCATGCGT
  TTGATCGAACAGCA
  TTCATACAAAACAG
  TTGATAATCATTTT
  TTGATCCTGCTACA
  TTAATTGCAATGGT
  GTGTTTTCATGGAA
  TTGATTGGTGTGAG
  TTGACGAGATCGAT
  TTCTTATAAATGCA
  TTAGTCAAAATGAT
  TAAATTTATTTGAA
  TTGATGACATAAGC
  GTGACGATACATTC
  TTATCTTATCGTTT

Position weight matrix (PWM). FNR matrix-quality result    
A	0	2	10	77	0	29	17	29	38	57	12	2	66	49
C	1	0	2	0	17	15	8	18	5	16	4	63	6	14
G	6	1	76	2	0	22	9	14	26	2	17	11	8	8
T	81	85	0	9	71	22	54	27	19	13	55	12	8	17

Consensus    
;	consensus.strict             	TTGAtgtaaatCaa
;	consensus.strict.rc          	TTGATTTACATCAA
;	consensus.IUPAC              	TTGAtrtwratCaa
;	consensus.IUPAC.rc           	TTGATYWAYATCAA
;	consensus.regexp             	TTGAt[ag]t[at][ag]atCaa
;	consensus.regexp.rc          	TTGAT[CT][AT]A[CT]ATCAA

PWM logo   


 


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
TF-target gene evolutionary conservation
Promoter-target gene evolutionary conservation


Evidence    

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

 [EXP-CHIP-SEQ] high throughput ChIP-seq evidence

 [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts

 [EXP-IMP-SITE-MUTATION] Site mutation

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-IEP-MICROARRAY] high throughput expression microarray evidence

 [COMP-AINF-PATTERN-DISCOVERY] Automated inference based on sequence pattern discovery

 [EXP-CHIP-CHIP] high throughput ChIP-chip evidence


Reference(s)    

 [1] Quail MA., Haydon DJ., Guest JR., 1994, The pdhR-aceEF-lpd operon of Escherichia coli expresses the pyruvate dehydrogenase complex., Mol Microbiol 12(1):95-104

 [2] Shalel-Levanon S., San KY., Bennett GN., 2005, Effect of ArcA and FNR on the expression of genes related to the oxygen regulation and the glycolysis pathway in Escherichia coli under microaerobic growth conditions., Biotechnol Bioeng 92(2):147-59

 [3] Cunningham L., Gruer MJ., Guest JR., 1997, Transcriptional regulation of the aconitase genes (acnA and acnB) of Escherichia coli., Microbiology 143 ( Pt 12):3795-805

 [4] Salmon K., Hung SP., Mekjian K., Baldi P., Hatfield GW., Gunsalus RP., 2003, Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR., J Biol Chem 278(32):29837-55

 [5] Membrillo-Hernandez J., Lin EC., 1999, Regulation of expression of the adhE gene, encoding ethanol oxidoreductase in Escherichia coli: transcription from a downstream promoter and regulation by fnr and RpoS., J Bacteriol 181(24):7571-9

 [6] Myers KS., Yan H., Ong IM., Chung D., Liang K., Tran F., Keles S., Landick R., Kiley PJ., 2013, Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding., PLoS Genet 9(6):e1003565

 [7] Constantinidou C., Hobman JL., Griffiths L., Patel MD., Penn CW., Cole JA., Overton TW., 2006, A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth., J Biol Chem 281(8):4802-15

 [8] Jennings MP., Beacham IR., 1993, Co-dependent positive regulation of the ansB promoter of Escherichia coli by CRP and the FNR protein: a molecular analysis., Mol Microbiol 9(1):155-64

 [9] Compan I., Touati D., 1994, Anaerobic activation of arcA transcription in Escherichia coli: roles of Fnr and ArcA., Mol Microbiol 11(5):955-64

 [10] Kumar R., Shimizu K., 2011, Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures., Microb Cell Fact 10:3

 [11] Spiro S., Guest JR., 1991, Adaptive responses to oxygen limitation in Escherichia coli., Trends Biochem Sci 16(8):310-4

 [12] Golby P., Kelly DJ., Guest JR., Andrews SC., 1998, Transcriptional regulation and organization of the dcuA and dcuB genes, encoding homologous anaerobic C4-dicarboxylate transporters in Escherichia coli., J Bacteriol 180(24):6586-96

 [13] Eichler K., Buchet A., Lemke R., Kleber HP., Mandrand-Berthelot MA., 1996, Identification and characterization of the caiF gene encoding a potential transcriptional activator of carnitine metabolism in Escherichia coli., J Bacteriol 178(5):1248-57

 [14] Scheu PD., Witan J., Rauschmeier M., Graf S., Liao YF., Ebert-Jung A., Basche T., Erker W., Unden G., 2012, CitA/CitB two-component system regulating citrate fermentation in Escherichia coli and its relation to the DcuS/DcuR system in vivo., J Bacteriol 194(3):636-45

 [15] Cotter PA., Gunsalus RP., 1992, Contribution of the fnr and arcA gene products in coordinate regulation of cytochrome o and d oxidase (cyoABCDE and cydAB) genes in Escherichia coli., FEMS Microbiol Lett 70(1):31-6

 [16] Cotter PA., Melville SB., Albrecht JA., Gunsalus RP., 1997, Aerobic regulation of cytochrome d oxidase (cydAB) operon expression in Escherichia coli: roles of Fnr and ArcA in repression and activation., Mol Microbiol 25(3):605-15

 [17] Fu HA., Iuchi S., Lin EC., 1991, The requirement of ArcA and Fnr for peak expression of the cyd operon in Escherichia coli under microaerobic conditions., Mol Gen Genet 226(1-2):209-13

 [18] Govantes F., Albrecht JA., Gunsalus RP., 2000, Oxygen regulation of the Escherichia coli cytochrome d oxidase (cydAB) operon: roles of multiple promoters and the Fnr-1 and Fnr-2 binding sites., Mol Microbiol 37(6):1456-69

 [19] Ramseier TM., Chien SY., Saier MH., 1996, Cooperative interaction between Cra and Fnr in the regulation of the cydAB operon of Escherichia coli., Curr Microbiol 33(4):270-4

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