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IHF DNA-binding transcriptional dual regulator

Synonyms: IHF
Summary:
IHF, "Integration host factor," is a global regulatory protein that helps to maintain DNA architecture. It binds and bends DNA at specific sites. IHF plays a role in DNA supercoiling and DNA duplex destabilization and affects processes such as DNA replication, recombination, and the expression of many genes [46] IHF is highly abundant in the cell. Its total intracellular concentration varies with growth rate and is higher in exponential phase, with 6,000 dimers per cell, than in stationary phase (3,000 dimers per cell) [] IHF acts mostly as an accessory factor, stabilizing a correct nucleoprotein complex. For example, IHF was originally found to be required for the site-specific recombination of phage λ with the chromosome [] For this, IHF stabilizes the bending of the DNA to facilitate binding of the bivalent integrase molecules [] As another example, IHF stimulates transcription at σ54-dependent promoters.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
IHF Functional   [APPH], [GEA], [IEP], [IMP] [1], [2], [3], [4], [5], [6], [7]
Evolutionary Family: IHF
Sensing class: TFs for DNA-bending
Connectivity class: Global Regulator
Gene name: ihfA
  Genome position: 1795253-1795552
  Length: 300 bp / 99 aa
Operon name: thrS-infC-rpmI-rplT-pheMST-ihfA
TU(s) encoding the TF:
Transcription unit        Promoter
ihfA
ihfAp4
pheMST-ihfA
pheMp
thrS-infC-rpmI-rplT-pheMST-ihfA
thrSp
Gene name: ihfB
  Genome position: 963828-964112
  Length: 285 bp / 94 aa
Operon name: cmk-rpsA-ihfB
TU(s) encoding the TF:
Transcription unit        Promoter
ihfB
ihfBp
rpsA-ihfB
rpsAp1
rpsA-ihfB
rpsAp3


Regulon       
Regulated gene(s) aceA, aceB, aceK, acs, actP, adiA, amiA, atoA, atoB, atoD, atoE, carA, carB, csgD, csgE, csgF, csgG, csrB, cysG, cysH, cysI, cysJ, dcuD, dmsA, dmsB, dmsC, dppA, dppB, dppC, dppD, dppF, dps, dusB, envZ, fhlA, fimA, fimB, fimC, fimD, fimF, fimG, fimH, fimI, fis, flhC, flhD, fliA, fliZ, fnr, focA, folA, gcd, glcA, glcB, glcD, glcE, glcF, glcG, glmY, glnH, glnP, glnQ, glpQ, glpT, gltA,
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Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
membrane (43)
anaerobic respiration (35)
carbon compounds (21)
Transcription related (19)
aerobic respiration (16)
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Regulated operon(s) aceBAK, acs-yjcH-actP, adiA, amiA-hemF, atoDAEB, bdm-sra, carAB, cmk-rpsA-ihfB, csgDEFG, csrB, cysJIH, dcuD, dmsABC, dppABCDF, dps, dusB-fis, fimAICDFGH, fimB, flhDC, fliAZ-tcyJ, fnr, focA-pflB, folA, gcd, glcDEFGBA, glmY, glnHPQ, glpTQ, gltA, gltBDF, hemA-prfA-prmC, hipBA, hpt, hycABCDEFGHI, hypABCDE-fhlA, ibpAB, ilvLXG_1G_2MEDA, micF, mtr, narGHJI, narK, ndh, nirBDC-cysG, nmpC, norVW, nrfABCDEFG, nuoABCEFGHIJKLMN, ompC, ompF, ompR-envZ, osmE, osmY, paaABCDEFGHIJK, paaZ, patA, proVWX, pspABCDE, pspG, pstSCAB-phoU, rpoH, rseD-rpoE-rseABC, rtcBA, sdhCDAB-sucABCD, sodA, sodB,
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First gene in the operon(s) aceB, acs, acs, adiA, amiA, atoD, carA, csgD, csrB, cysJ, dcuD, dmsA, dppA, dps, dusB, fimA, fimB, flhD, fliA, fnr, focA, folA, gcd, glcD, glmY, glnH, glpT, gltA, gltB, hemA, hemF, hipB, hpt, hycA, hypA, hypA, ibpB, ihfA, ihfB, ilvL, ilvL, ilvL, ilvL, micF, mtr, narG, narK, ndh, nirB, nmpC, norV, nrfA, nuoA, ompC, ompC, ompF, ompR, osmE, osmY, paaA, paaZ, patA, proV, pspA, pspG,
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Simple and complex regulons AcrR,CRP,FliZ,Fur,H-NS,HdfR,IHF,LrhA,MatA,OmpR,QseB,RcsAB,YjjQ
AcrR,H-NS,HU,IHF,Lrp,MarA,OmpR,Rob,SoxS
AdiY,ArgR,CRP,FNR,Fur,GadE,HdfR,IHF,Lrp,Nac
AdiY,H-NS,IHF
ArcA,CRP,Cra,IHF,IclR
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Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[IHF,-](32)
[IHF,+-](1)
[IHF,+](46)


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 (Confirmed, Strong, Weak) References
  IHF activator aceBp Sigma70 -159.0 -235.0 aceB, aceA, aceK
tcgttaagcgATTCAGCACCTTAcctcaggcac
4215237 4215249 [BPP], [GEA] [8]
  IHF activator aceBp Sigma70 -72.0 -148.0 aceB, aceA, aceK
ttcatattgtTATCAACAAGTTAtcaagtattt
4215324 4215336 [BPP], [GEA] [8]
  IHF repressor acsp1 Sigma70 -21.0 -245.0 acs, yjcH, actP
tggtattttaCATGCACTTACAAttgattaaag
4287610 4287622 [BPP], [GEA] [9], [10]
  IHF repressor acsp2 Sigma70, Sigma38 -225.0 -245.0 acs, yjcH, actP
tggtattttaCATGCACTTACAAttgattaaag
4287610 4287622 [BPP], [GEA] [9], [10], [11]
  IHF repressor acsp2 Sigma70, Sigma38 -180.0 -200.0 acs, yjcH, actP
tatgcatgctGTTGAAAAAGAGGaagatactga
4287565 4287577 [AIBSCS], [BPP], [GEA] [9]
  IHF repressor acsp2 Sigma70, Sigma38 -153.0 -173.0 acs, yjcH, actP
tgattaattcTTTGAGGAACATGcagttatgca
4287538 4287550 [AIBSCS], [BPP], [GEA], [SM] [9], [12], [13]
  IHF activator adiAp Sigma70 nd 4340521.0 adiA nd nd [GEA], [SM] [14]
  IHF repressor amiAp Sigma70 20.5 -92.0 amiA, hemF
tgtcaactatTGAAATGAAAAGTaaaacaattc
2552254 2552266 [HIBSCS] [15]
  IHF activator atoDp Sigma54 -57.0 -92.0 atoD, atoA, atoE, atoB
cccttcatatTCAATTAGTTAAAtaactaaatc
2323349 2323361 [GEA], [HIBSCS] [16]
  IHF activator atoDp Sigma54 -32.0 -67.0 atoD, atoA, atoE, atoB
actaaatccaATAATCTCATTCTggcactcccc
2323374 2323386 [GEA], [HIBSCS], [SM] [16]
  IHF dual carAp1 Sigma70 -305.0 -405.0 carA, carB
atttaatttaTTGATTATAAAGGgctttaattt
29240 29252 [BCE], [BPP], [GEA], [HIBSCS], [SM] [17], [18], [19]
  IHF dual carAp1 Sigma70 -305.0 -405.0 carA, carB
atttaatttaTTGATTATAAAGGgctttaattt
29240 29252 [BCE], [BPP], [GEA], [HIBSCS], [SM] [17], [18], [19]
  IHF activator csgDp1 Sigma38, Sigma70 -173.5 -322.0 csgD, csgE, csgF, csgG
aaaatcatacAAATGGTGATAACTTACTAATAATGCATATaaaaaatatt
1103503 1103533 [BPP], [GEA] [20], [21]
  IHF activator csgDp1 Sigma38, Sigma70 -66.5 -215.0 csgD, csgE, csgF, csgG
aaatcaagtgTTAAACATGTAACTAAATGTAACTCGTTATATTAAAATGTTAACCTTAAGGTTTTATTAAgtttagaaat
1103381 1103441 [BPP], [GEA] [21]
  IHF activator csrBp Sigma70 -99.0 -99.0 csrB
aattaacaatCAACATTTTGATTttaaatgaaa
2924617 2924629 [AIBSCS], [GEA] [22]
  IHF activator cysJp Sigma70 -124.0 -190.0 cysJ, cysI, cysH
taaccaacctAATGAAAAACAAAtgaatttagc
2892082 2892094 [BPP], [GEA] [23]
  IHF activator dcuDp2 Sigma54 -44.0 -330.0 dcuD
acatcctatcACAGGATTGAAAGtaggggaaaa
3374533 3374545 [HIBSCS] [24], [25]
  IHF repressor dmsAp2 nd -22.0 -103.0 dmsA, dmsB, dmsC
tctctttgatTTTCAAATTATTCgatgtataca
940850 940862 [BPP], [GEA], [HIBSCS] [26]
  IHF activator dppAp Sigma70 1848.0 1682.0 dppA, dppB, dppC, dppD, dppF
aaattcaataCATTGCAGAATTTtcgtaggcct
3706017 3706029 [BCE] [27]
  IHF activator dpsp Sigma70, Sigma38 -98.5 -137.0 dps
caaaactaatAAAGATTCAATGAgttagatata
849042 849054 [HIBSCS] [28]
  IHF activator dusBp Sigma70 -114.0 -148.0 dusB, fis
tttctaatatGATGATTTTTATGagtaattatc
3410126 3410138 [BPP], [GEA], [HIBSCS], [SM] [29], [30]
  IHF activator fimAp Sigma70 -52.0 -473.0 fimA, fimI, fimC, fimD, fimF, fimG, fimH
aggtttgattTAACTTATTGATAataaagttaa
4542636 4542648 [GEA], [HIBSCS] [31], [32], [33], [34]
  IHF activator fimAp Sigma70 77.0 -345.0 fimA, fimI, fimC, fimD, fimF, fimG, fimH
aaaaagcatcTAACTGTTTGATAtgtaaattat
4542764 4542776 [GEA], [HIBSCS] [31], [32], [33], [34]
  IHF activator fimBp2 nd -576.0 -866.0 fimB
agatcttagtTTAACTATTTGTTttataaataa
4540085 4540097 [BPP], [HIBSCS], [SM] [35]
  IHF repressor flhDp Sigma70 -92.0 -290.0 flhD, flhC
cacacaaaacACTCAATTACTTAacataaatgg
1978481 1978493 [HIBSCS] [36]
  IHF repressor fliAp1 Sigma70 -202.5 -233.0 fliA, fliZ, tcyJ
aaatgtgcaaATTCAATAAATTGCAAttcaacttgt
2002014 2002030 [GEA], [IHBCE], [SM] [20]
  IHF repressor fliAp1 Sigma70 -186.5 -217.0 fliA, fliZ, tcyJ
cttatccggcCTACAAAAATGTGCAAattcaataaa
2001998 2002014 [GEA], [IHBCE], [SM] [20]
  IHF activator fnrp Sigma70 -104.0 -130.0 fnr
gtctatctatTTGAAAACCCTTAAgttgttaagg
1399649 1399663 [BPP], [GEA], [SM] [37]
  IHF activator focAp1 Sigma70 -112.5 -139.0 focA, pflB
acggagtaaaTATTTGATTATCCaaataaaaat
954599 954611 [BCE], [BPP], [GEA], [HIBSCS], [SM] [38]
  IHF activator folAp Sigma70 -65.0 -89.0 folA
tcgccagcagAATATAAAATTTTcctcaacatc
49728 49740 [GEA], [HIBSCS] [39]
  IHF activator gcdp1 Sigma70 -73.0 -111.0 gcd
agattccgcgAATGAATAGTTTTactggtatac
141330 141342 [GEA], [HIBSCS], [SM] [40]
  IHF activator glcDp Sigma70 -107.0 -162.0 glcD, glcE, glcF, glcG, glcB, glcA
ggttaactcaATGTTAAATTGATgtaacataat
3128177 3128189 [BCE], [GEA] [41]
  IHF activator glmYp1 Sigma54 -169.0 -169.0 glmY
agataatattAAAATCAATGAGTtaagtgtcgc
2691503 2691515 [BPP], [GEA], [HIBSCS], [SM] [42], [43]
  IHF activator glmYp1 Sigma54 -52.0 -52.0 glmY
aatagtttggTAACGTACTGATTatacgttgct
2691386 2691398 [BPP], [GEA], [HIBSCS] [42]
  IHF activator glnHp2 Sigma54 -152.0 -195.0 glnH, glnP, glnQ
attgtgcactCAACACAGTGATTatttagcgta
848193 848205 [HIBSCS] [44], [45], [46]
  IHF activator glnHp2 Sigma54 -47.0 -90.0 glnH, glnP, glnQ
ttgcaactccTTGATTTTTCGAGatgcggcaaa
848088 848100 [BPP], [HIBSCS], [SM] [44], [45]
  IHF repressor glpTQp Sigma70 35.0 -43.0 glpT, glpQ
atttatgattAACAGCCTGATTCagtgagagaa
2352411 2352423 [BPP], [GEA], [HIBSCS] [47]
  IHF repressor glpTQp Sigma70 202.0 124.0 glpT, glpQ
gttcttacgaACCAAATAGTAAGccgcatagcc
2352244 2352256 [BPP], [GEA], [HIBSCS] [47]
  IHF activator gltAp1 Sigma70 -70.0 -369.0 gltA
aatgattgtcAAATTAGATGATTaaaaattaaa
754831 754843 [AIBSCS], [BCE], [GEA] [48], [49], [50]
  IHF activator gltBp Sigma70 -89.0 -305.0 gltB, gltD, gltF
tccattttaaTTTCAGTCATTTAataaagaatt
3354414 3354426 [BPP], [GEA] [51], [52]
  IHF activator gltBp Sigma70 -85.0 -301.0 gltB, gltD, gltF
ttttaatttcAGTCATTTAATAAagaattttgc
3354418 3354430 [BPP], [GEA] [51], [52]
  IHF activator hemAp1 Sigma70 nd -1263714.0 hemA, prfA, prmC nd nd [GEA] [53]
  IHF repressor hemFp Sigma70 8.0 -13.0 hemF
agaaagcacaTTCGAAAAAGCGAtaagttatga
2553206 2553218 [HIBSCS] [15]
  IHF activator hipBp Sigma70 -117.0 -157.0 hipB, hipA
aggatttaaaTAAGGCGTTGATGcgccgtttga
1592593 1592605 [HIBSCS] [54]
  IHF repressor hptp Sigma70 -24.0 -95.0 hpt
gtataccagtAAAACTATTCATTcgcggaatct
141330 141342 [GEA], [HIBSCS], [SM] [40]
  IHF activator hycAp Sigma54 -38.5 -64.0 hycA, hycB, hycC, hycD, hycE, hycF, hycG, hycH, hycI
atctctttaaTAACAATAAATTAaaagttggca
2850493 2850505 [BPP], [GEA], [HIBSCS] [55]
  IHF activator hypAp Sigma54 -127.5 -148.0 hypA, hypB, hypC, hypD, hypE, fhlA
tgccaactttTAATTTATTGTTAttaaagagat
2850493 2850505 [BPP], [GEA], [HIBSCS] [55]
  IHF activator ibpBp Sigma54 -31.0 -115.0 ibpB
cggccttaggGAATTAGTTGATTtcgatacggc
3867006 3867018 [AIBSCS] [56]
  IHF repressor ihfAp4 Sigma38 -47.0 -216.0 ihfA
gccaactttcTTACATTCGGATAaaatatccgc
1795762 1795774 [BPP], [HIBSCS] [1], [57]
  IHF repressor ihfAp4 Sigma38 -21.0 -190.0 ihfA
aagtttacgcCAACTACCTGATTtacgccaact
1795736 1795748 [BPP], [HIBSCS] [1], [57]
  IHF repressor ihfAp4 Sigma38 54.0 -116.0 ihfA
tatcttgcagGATCAGGCTTATGgcgaggctct
1795662 1795674 [BPP], [HIBSCS] [1], [57]
  IHF repressor ihfBp Sigma38, Sigma70 -320.0 -399.0 ihfB
cgttgaaggtTACCTGCGTGCTTctgaagcatc
963423 963435 [BPP], [GEA] [1], [57]
  IHF repressor ihfBp Sigma38, Sigma70 -304.0 -383.0 ihfB
cgtgcttctgAAGCATCCCGTGAccgcgttgaa
963439 963451 [BPP], [GEA] [1], [57]
  IHF repressor ihfBp Sigma38, Sigma70 -207.0 -286.0 ihfB
aaaaccgcgcAATCAGCCTGTCTgttcgtgcga
963536 963548 [BPP], [GEA] [1], [57]
  IHF repressor ihfBp Sigma38, Sigma70 -157.0 -236.0 ihfB
aaagatgcaaTCGCAACTGTTAAcaaacaggaa
963586 963598 [BPP], [GEA] [1], [57]
  IHF repressor ihfBp Sigma38, Sigma70 -77.0 -156.0 ihfB
taaaggcgagTAATTCTCTGACTcttcgggatt
963666 963678 [BPP], [GEA] [1], [57]
  IHF repressor ihfBp Sigma38, Sigma70 -2.0 -81.0 ihfB
ttcgtcctgtAATCAAGCACTAAgggcggctac
963741 963753 [BPP], [GEA] [1], [57]
  IHF repressor ilvLp1 Sigma70 -17.0 -121.0 ilvL, ilvX, ilvG_1, ilvG_2, ilvM, ilvE, ilvD, ilvA
tatttttaaaAAACAACAATTTAtattgaaatt
3950195 3950207 [BPP], [GEA], [SM] [58]
  IHF repressor ilvLp1 Sigma70 210.0 105.0 ilvL, ilvX, ilvG_1, ilvG_2, ilvM, ilvE, ilvD, ilvA
aaaggcttagAGATCAAGCCTTAacgaactaag
3950421 3950433 [BPP], [GEA], [HIBSCS] [58]
  IHF activator ilvLp2 Sigma70 -89.0 -121.0 ilvL, ilvX, ilvG_1, ilvG_2, ilvM, ilvE, ilvD, ilvA
tatttttaaaAAACAACAATTTAtattgaaatt
3950195 3950207 [BPP], [GEA], [SM] [58], [59], [60], [61], [62]
  IHF activator ilvLp2 Sigma70 138.0 105.0 ilvL, ilvX, ilvG_1, ilvG_2, ilvM, ilvE, ilvD, ilvA
aaaggcttagAGATCAAGCCTTAacgaactaag
3950421 3950433 [BPP], [GEA], [HIBSCS] [58], [59], [62]
  IHF repressor micFp Sigma70 -72.0 -72.0 micF
tacttaagaaTAAGTTATTGATTttaaccttga
2313006 2313018 [BCE], [BPP], [GEA], [HIBSCS] [63]
  IHF repressor mtrp2 Sigma70 nd 3305817.0 mtr nd nd [GEA] [64]
  IHF activator narGp Sigma70 -125.0 -182.0 narG, narH, narJ, narI
aaacgtcttaATTTACAGTCTGTtatgtggtgg
1279676 1279688 [BCE], [BPP], [GEA], [HIBSCS] [65], [66], [67]
  IHF activator narKp1 Sigma70 -130.0 -155.0 narK
ttttacagcaCCGTGAAAAATCTcataattttt
1277796 1277808 [BPP], [GEA] [68], [69]
  IHF repressor ndhp Sigma70 -58.0 -151.0 ndh
cttttcagcaACAAAACTTGATTaacatcaatt
1165928 1165940 [BCE], [BPP], [GEA], [HIBSCS] [70]
  IHF repressor ndhp Sigma70 -17.0 -110.0 ndh
accaatgcacCATTCATGTTATTctcaatagcg
1165969 1165981 [BCE], [BPP], [GEA], [HIBSCS] [70]
  IHF repressor ndhp Sigma70 26.0 -68.0 ndh
ttcattgctgTAACCTGTTGTTAattaagagct
1166011 1166023 [BCE], [BPP], [GEA], [HIBSCS] [70]
  IHF activator nirBp Sigma70 -115.0 -139.0 nirB, nirD, nirC, cysG
catgaaatatCAGACAATTCCGTgacttaagaa
3493866 3493878 [BPP], [GEA], [HIBSCS] [71], [72]
  IHF repressor nirBp Sigma70 -88.0 -112.0 nirB, nirD, nirC, cysG
taagaaaattTATACAAATCAGCaatataccca
3493893 3493905 [BCE], [BPP], [GEA] [71], [72], [73]
  IHF repressor nmpCp nd -144.0 -189.0 nmpC
gctgaataaaAATAAATCTATTAgccaatttat
577008 577020 [HIBSCS], [SM] [74]
  IHF activator norVp Sigma54 -48.0 -85.0 norV, norW
aattttatttATAGAGTAAAAACaatcagataa
2832385 2832397 [BPP] [75]
  IHF repressor norVp Sigma54 17.0 -21.0 norV, norW
catctttttaGAACACGCTGAATaaattgaggt
2832449 2832461 [BPP] [75]
  IHF activator nrfAp Sigma70 -127.0 -220.0 nrfA, nrfB, nrfC, nrfD, nrfE, nrfF, nrfG
tgcataactgCATGTTCCTCAAAgaattaatca
4287538 4287550 [AIBSCS], [BPP], [GEA], [SM] [9], [12], [13]
  IHF repressor nrfAp Sigma70 -55.0 -148.0 nrfA, nrfB, nrfC, nrfD, nrfE, nrfF, nrfG
ctttaatcaaTTGTAAGTGCATGtaaaatacca
4287610 4287622 [BPP], [GEA] [9], [10], [11]
  IHF repressor nuoAp2 Sigma70 -83.0 -173.0 nuoA, nuoB, nuoC, nuoE, nuoF, nuoG, nuoH, nuoI, nuoJ, nuoK, nuoL, nuoM, nuoN
ttgtcaacttTAACAAAAGTTTCttcacattag
2405239 2405251 [BPP], [GEA], [HIBSCS], [SM] [76], [77]
  IHF repressor nuoAp2 Sigma70 -74.0 -164.0 nuoA, nuoB, nuoC, nuoE, nuoF, nuoG, nuoH, nuoI, nuoJ, nuoK, nuoL, nuoM, nuoN
tataacctttTGTCAACTTTAACaaaagtttct
2405230 2405242 [BPP], [GEA], [HIBSCS] [76], [77]
  IHF repressor nuoAp2 Sigma70 -66.0 -156.0 nuoA, nuoB, nuoC, nuoE, nuoF, nuoG, nuoH, nuoI, nuoJ, nuoK, nuoL, nuoM, nuoN
ctcctttctaTAACCTTTTGTCAactttaacaa
2405222 2405234 [BPP], [GEA], [HIBSCS] [76], [77]
  IHF repressor ompCp1 Sigma70 -182.0 -263.0 ompC
tcaaggttaaAATCAATAACTTAttcttaagta
2313006 2313018 [BCE], [BPP], [GEA], [HIBSCS] [63]
  IHF repressor ompCp3 nd -125.0 -263.0 ompC
tcaaggttaaAATCAATAACTTAttcttaagta
2313006 2313018 [BCE], [BPP], [GEA], [HIBSCS] [63]
  IHF repressor ompFp Sigma38, Sigma70 -176.0 -286.0 ompF
aattttaatcTATTTATATGATTtccttatatt
987262 987274 [BCE], [HIBSCS] [78]
  IHF activator ompFp Sigma38, Sigma70 -108.0 -218.0 ompF
aaaagtaaaaTTTAAGGAACTTTgtgaacaccg
987194 987206 [BCE], [HIBSCS] [78]
  IHF repressor ompFp Sigma38, Sigma70 -62.0 -172.0 ompF
gctacaaagaTAAAGATTTGGTTtcaaaaagaa
987148 987160 [BCE], [HIBSCS] [78]
  IHF repressor ompRp1 Sigma70 -102.0 -225.0 ompR, envZ
gacaaagggaATCAACGAGATGAaaacgcccct
3536803 3536815 [BPP], [SM] [79]
  IHF repressor ompRp1 Sigma70 -37.0 -160.0 ompR, envZ
tcggcgaaacATTATTGATTCTGttgatatgat
3536738 3536750 [BPP], [SM] [79]
  IHF repressor ompRp1 Sigma70 8.0 -116.0 ompR, envZ
ttgttacaaaGCATATTAAACAGcagcttaagt
3536694 3536706 [BPP], [SM] [79]
  IHF repressor osmEp Sigma70, Sigma38 4.5 -23.0 osmE
tcctcttgttTATCAGCGTGTTAgataagcctg
1822273 1822285 [GEA], [HIBSCS] [80]
  IHF repressor osmYp Sigma70, Sigma38 -96.5 -340.0 osmY
tcaatttcccTTCCTTATTAGCCgcttacggaa
4611050 4611062 [BPP], [GEA], [HIBSCS] [81], [82]
  IHF repressor osmYp Sigma70, Sigma38 -5.0 -248.0 osmY
ttgtgatctaTATTTAACAAAGTgatgacattt
4611142 4611154 [BCE], [GEA] [82]
  IHF activator paaAp Sigma70 -115.0 -177.0 paaA, paaB, paaC, paaD, paaE, paaF, paaG, paaH, paaI, paaJ, paaK
attaatgtttTCCGCAGTTGCTAtacagatcgc
1453744 1453756 [BPP], [GEA], [HIBSCS], [SM] [83]
  IHF activator paaZp nd -80.0 -108.0 paaZ
gcgatctgtaTAGCAACTGCGGAaaacattaat
1453744 1453756 [BPP], [GEA], [HIBSCS], [SM] [83]
  IHF unknown patAp Sigma38, Sigma54 -256.0 -292.0 patA
tttaaacacaAATCTAATTCCTTgatttaaaat
3219196 3219208 [AIBSCS] [84]
  IHF activator proVp3 Sigma70 -18.5 -78.0 proV, proW, proX
ttgcctcagaTTCTCAGTATGTTAgggtagaaaa
2804730 2804744 [BPP], [GEA] [85]
  IHF activator proVp3 Sigma70 140.0 79.5 proV, proW, proX
gttcaaatatATCGAACAAGGACTTtcaaaagaac
2804887 2804902 [BPP], [GEA] [85]
  IHF activator pspAp Sigma54 -42.5 -84.0 pspA, pspB, pspC, pspD, pspE
atcagatcttTATAAATCAAAAAgataaaaaat
1367989 1368001 [BCE], [BPP], [GEA], [HIBSCS] [86], [87]
  IHF activator pspGp Sigma54 -38.5 -63.0 pspG
ttttgctgttAAATCAATAGATTatttttggca
4262771 4262783 [ICA] [88]
  IHF activator pstSp Sigma70, Sigma38 16.5 -27.0 pstS, pstC, pstA, pstB, phoU
gggaggattcATAAAGCATTGTTtgttggctac
3911546 3911558 [BPP], [GEA] [89], [90], [91]
  IHF repressor rpoEp1b Sigma70 -59.5 -289.0 rseD, rpoE, rseA, rseB, rseC
acattcatgtGACGTGTTGATTatcggtagcg
2710447 2710459 [GEA], [HIBSCS], [IC] [20], [92]
  IHF activator rpoHp6 Sigma54 -326.0 -356.0 rpoH
catcgaatgaTAAGCCATTGATAtcaaacttcg
3601133 3601145 [BPP], [GEA] [93]
  IHF activator rtcBp Sigma54 -62.0 -90.0 rtcB, rtcA
taattttttaATTCATTGTTTTAaaaaagatta
3558163 3558175 [AIBSCS] [94]
  IHF activator rtcBp Sigma54 -52.0 -80.0 rtcB, rtcA
ataagcagctTAATTTTTTAATTcattgtttta
3558153 3558165 [AIBSCS] [94]
  IHF repressor sodAp Sigma70 -68.0 -119.0 sodA
cattttcctgCAAAACCATACCCttacgaaaag
4100685 4100697 [BPP], [HIBSCS] [5]
  IHF repressor sodAp Sigma70 -48.0 -99.0 sodA
cccttacgaaAAGTACGGCATTGataatcattt
4100705 4100717 [BPP], [HIBSCS] [5]
  IHF repressor sodAp Sigma70 -24.0 -75.0 sodA
taatcattttCAATATCATTTAAttaactataa
4100729 4100741 [BPP], [HIBSCS] [5]
  IHF repressor sodAp Sigma70 -1.0 -52.0 sodA
ttaactataaTGAACCAACTGCTtacgcggcat
4100752 4100764 [BPP], [HIBSCS] [5]
  IHF repressor sodBp Sigma70 -61.0 -116.0 sodB
gctaaaacttTACCCTGTTGTTAcggcaacagg
1735256 1735268 [AIBSCS], [GEA] [95]
  IHF activator srap Sigma38 nd 1555963.0 sra nd nd [GEA] [96]
  IHF activator ssuEp Sigma70 -177.0 -228.0 ssuE, ssuA, ssuD, ssuC, ssuB
atattcatgaAATCTATAAATTAaagatttgtc
997734 997746 [BPP], [GEA], [HIBSCS] [97]
  IHF activator ssuEp Sigma70 -134.0 -185.0 ssuE, ssuA, ssuD, ssuC, ssuB
ttagatgttgAATCAATGAATTActcgttcagt
997691 997703 [BPP], [GEA], [HIBSCS] [97]
  IHF repressor ssuEp Sigma70 33.0 -19.0 ssuE, ssuA, ssuD, ssuC, ssuB
tctctccttaTAACCAATTGTTCtttttttgtt
997525 997537 [BPP], [GEA], [HIBSCS] [97]
  IHF repressor sucAp Sigma38 nd -758706.0 sucA, sucB, sucC, sucD nd nd [AIBSCS], [GEA] [48], [49]
  IHF activator sufAp Sigma70 -145.0 -177.0 sufA, sufB, sufC, sufD, sufS, sufE
attaggtatcTCATTGTTAGATAatggttatta
1764557 1764569 [BPP], [SM] [98], [99]
  IHF activator tdcAp nd -103.0 -131.0 tdcA, tdcB, tdcC, tdcD, tdcE, tdcF, tdcG
acaattaaatACCTTTAAATATCaacaagttaa
3267190 3267202 [BCE], [BPP], [HIBSCS], [SM] [100], [101]
  IHF repressor tyrPp1 Sigma70 nd -1989681.0 tyrP nd nd [GEA] [64]
  IHF repressor ubiCp Sigma70 -12.0 -75.0 ubiC, ubiA
ttgcgtattaGATCACTTAATTTgctttacatc
4252425 4252437 [GEA], [HIBSCS] [102]
  IHF repressor ulaAp Sigma70 nd -4419980.0 ulaA, ulaB, ulaC, ulaD, ulaE, ulaF nd nd [BCE], [NTAS] [103]
  IHF repressor ulaGp nd nd 4419625.0 ulaG nd nd [BCE], [GEA] [103]
  IHF activator uspAp1 Sigma70 -81.0 -209.0 uspA
ttttcgacatGAATATATTGATAgtggttaacc
3639896 3639908 [GEA], [HIBSCS] [104], [105]
  IHF repressor uspBp Sigma38 -54.0 -182.0 uspB
ggttaaccacTATCAATATATTCatgtcgaaaa
3639896 3639908 [GEA], [HIBSCS] [104]
  IHF activator yadVp1 Sigma70 nd 156201.0 yadV, htrE nd nd [GEA] [106]
  IHF activator yadVp2 Sigma38 nd 156201.0 yadV, htrE nd nd [GEA] [106]
  IHF activator yadVp3 Sigma70 nd 156201.0 yadV, htrE nd nd [GEA] [106]
  IHF activator yeiLp Sigma38 -227.0 -292.0 yeiL
aatgttttatCAAGCGTCTGATTacccgctaca
2255057 2255069 [GEA], [HIBSCS] [107]
  IHF activator yeiLp Sigma38 -193.0 -258.0 yeiL
tagtgatgccTAATAAATCTATTgccggatgtt
2255091 2255103 [GEA], [HIBSCS] [107]
  IHF repressor yiaJp Sigma70 -4.0 -90.0 yiaJ
tttttatgtcTTTTGAAATTCATcaatcagatt
3742616 3742628 [BPP], [HIBSCS] [108]
  IHF activator yiaKp Sigma70 -49.5 -109.0 yiaK, yiaL, yiaM, yiaN, yiaO, lyxK, sgbH, sgbU, sgbE
tttatgtcttTTGAAATTCATCAatcagattgc
3742618 3742630 [BPP], [GEA], [HIBSCS], [SM] [108]
  IHF activator yjbEp1 Sigma70 -133.0 -181.0 yjbE, yjbF, yjbG, yjbH
tgtttttattTTAAGTTTATGATttttattgtt
4235719 4235731 [BPP], [HIBSCS] [109]


Alignment and PSSM for IHF TFBSs    

Aligned TFBS of IHF   
  Sequence
  AAAGCCCTTTATA
  AAAATTTTATATT
  GAATGAATAGTTT
  TAATAGATTTATT
  AAATTAGATGATT
  TCCTTGATTTTTC
  CAACACAGTGATT
  TAACTCATTGAAT
  GAATAATTTGAAA
  TAAATATTTGATT
  TACCTGCGTGCTT
  TCACGGGATGCTT
  AGACAGGCTGATT
  ATCGCAACTGTTA
  TAATTCTCTGACT
  TTAGTGCTTGATT
  TAAAGATTTGGTT
  AAAGTTCCTTAAA
  TAATCTATTTATA
  TAACCAATTGTTC
  TAATTCATTGATT