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ArcA DNA-binding transcriptional dual regulator

Synonyms: ArcA-Phosphorylated, ArcA
Summary:
ArcA is a dual transcriptional regulator for Anoxic redox control [5, 66, 67] It acts primarily as a negative transcriptional regulator under anaerobic conditions. ArcA represses operons involved in respiratory metabolism, including those that encode products such as the tricarboxylic acid cycle enzymes, enzymes of the glyoxylate shunt, and enzymes of the pathway for fatty acid degradation [67, 68, 69] In addition, ArcA acts as a repressor for rpoS transcription [58] ArcA also activates a few operons encoding proteins involved in fermentative metabolism [13, 42] It has been identified as global repressor of carbon oxidation pathways [55] Microarray analyses have identified a large number of genes affected by ArcA and have revealed that the Arc system and the FNR regulatory network overlap to a much greater extent than previously estimated [9, 22, 70] It has been suggested that the most significant role of ArcA is under microaerobic conditions, while that of FNR is under more strictly anaerobic conditions [71, 72] For full expression of arcA both FNR and ArcA are required [73] Distinct functional roles for both regulators have been proposed, and it has been shown that there is little direct coregulation of the two [55]
ArcA is a response regulator and is activated as a DNA-binding protein by phosphorylation [74] The cognate sensor kinase ArcB is membrane associated and has three cytoplasmic domains; a transmitter, a receiver, and a phosphotransfer (HPt) domain [75, 76] Under anaerobic conditions ArcA is phosphorylated in a phosphorelay reaction that involves phosphotransfer from the autophosphorylated transmitter domain of ArcB to the receiver and Hpt domain of ArcB and finally to the receiver domain of ArcA [1, 3, 77] Autophosphorylation of ArcB is stimulated by effectors such as d-lactate, pyruvate, and acetate [78, 78] Under aerobic conditions, the autokinase activity of ArcB is inhibited by quinone electron carriers [79, 80] and unphosphorylated ArcB promotes the dephosphorylation of ArcA-P by a reverse phosphorelay reaction [81, 82] It has been suggested that ArcA may also be subject to cross-regulation by other, unknown sensor kinases [58, 83, 84]
ArcA is a member of the OmpR/PhoB subfamily of response regulators and consists of an N-terminal receiver domain and a C-terminal helix-turn-helix DNA-binding domain [85] The crystal structures of the receiver domain of ArcA in the presence and absence of the phosphoryl analog BeF3- have been solved [86] In the crystal structures, the receiver domain forms a symmetric dimer.
Weight matrices for the DNA-binding site for ArcA-P have been obtained.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
ArcA Non-Functional   Apo [BPP], [IPI] [1], [2], [3], [4]
ArcA-Phosphorylated Functional Covalent Holo [BPP], [IPI] [1], [2], [3], [4]
Evolutionary Family: OmpR
Sensing class: External-Two-component systems
Connectivity class: Global Regulator
Gene name: arcA
  Genome position: 4639590-4640306
  Length: 717 bp / 238 aa
Operon name: arcA
TU(s) encoding the TF:
Transcription unit        Promoter
arcA
arcAp1
arcA
arcAp2
arcA
arcAp3
arcA
arcAp4
arcA
arcAp5
arcA
arcAp6
arcA
arcAp7


Regulon       
Regulated gene(s) aceA, aceB, aceE, aceF, aceK, ackA, acnA, acnB, aldA, appA, appB, appC, appX, arcZ, betA, betB, betI, betT, cadA, cadB, caiA, caiB, caiC, caiD, caiE, caiT, citC, citD, citE, citF, citG, citX, cydA, cydB, cydC, cydD, cyoA, cyoB, cyoC, cyoD, cyoE, dctA, dcuC, dpiA, dpiB, fadA, fadB, fadD, fadE, fadH, fadI, fadJ, fadL, fnr, focA, fumA, fumB, fumC, gadA, gadE, gadF, gadX, gatA, gatB, gatC,
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Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
membrane (48)
aerobic respiration (33)
anaerobic respiration (31)
electron donors (30)
carbon compounds (25)
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Regulated operon(s) aceBAK, ackA-pta, acnA, acnB, aldA, appCBXA, arcZ, betIBA, betT, cadBA, caiTABCDE, citCDEFXG, cydAB, cydDC, cyoABCDE, dctA, dcuB-fumB, dcuC, dpiBA, fadBA, fadD-sroD, fadE, fadH, fadIJ, fadL, fnr, focA-pflB, fumAC, gadAXW, gadEF-mdtEF, gatYZABCD, glcDEFGBA, glpABC, glpD, gltA, grcA, hemA-prfA-prmC, hyaABCDEF, hybOABCDEFG, icd, iraM, lldPRD, mdh, moeAB, ndh, nlpD-rpoS, nuoABCEFGHIJKLMN, ompW, oppABCDF, pdhR-aceEF-lpd, ptsG, puuAP, puuDRCBE, rhaT, rpsJ-rplCDWB-rpsS-rplV-rpsC-rplP-rpmC-rpsQ, rutABCDEFG, sdhCDAB-sucABCD, sodA, ssb, tpx, treBC, ubiCA, uvrA, xylFGHR, ybdN,
First gene in the operon(s) aceB, aceE, ackA, acnA, acnB, aldA, appC, arcZ, betI, betT, cadB, caiT, citC, cydA, cydA, cydA, cydA, cydD, cyoA, dctA, dcuC, dpiB, fadB, fadD, fadE, fadH, fadI, fadL, fnr, focA, focA, fumA, fumA, fumB, fumC, gadA, gadE, gadE, gatY, glcD, glpA, glpD, gltA, grcA, hemA, hyaA, hybO, icd, iraM, lldP, lpd, mdh, moeA, ndh, nuoA, ompW, oppA, ptsG, puuA, puuD, rhaT, rpoS, rpsJ, rutA, sdhC,
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Simple and complex regulons AdiY,ArcA,CRP,FNR,Fis,GadW,GadX,H-NS,RcsB,TorR
AppY,ArcA,Fis,IscR,NarL,NarP,YdeO
AppY,ArcA,YdeO
ArcA
ArcA,BetI,Cra
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Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[ArcA,-](38)
[ArcA,+](15)


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
  ArcA-Phosphorylated repressor aceBp Sigma70 nd nd aceB, aceA, aceK nd nd [RBM] [5]
  ArcA-Phosphorylated repressor aceEp Sigma70 nd nd aceE, aceF nd nd [GEA] [6]
  ArcA-Phosphorylated activator ackAp Sigma32 nd nd ackA nd nd [GEA] [6]
  ArcA-Phosphorylated repressor acnAp2 Sigma70 -34.0 -84.0 acnA
aatttgggttGTTATCAAATCGTTAcgcgatgttt
1335740 1335754 [GEA], [HIBSCS] [7]
  ArcA-Phosphorylated repressor acnBp Sigma70 -170.0 -266.0 acnB
gaggcggtagTTTAAATTTTGACTAatcttgggat
131342 131356 [GEA], [HIBSCS] [7]
  ArcA-Phosphorylated repressor acnBp Sigma70 -143.0 -239.0 acnB
cttgggattcGTTGAGAAAGGTGATtatcaccatg
131369 131383 [GEA], [HIBSCS] [7]
  ArcA-Phosphorylated repressor acnBp Sigma70 -139.0 -235.0 acnB
ggattcgttgAGAAAGGTGATTATCaccatgcgaa
131373 131387 [GEA], [HIBSCS] [7]
  ArcA-Phosphorylated repressor acnBp Sigma70 -119.0 -215.0 acnB
ttatcaccatGCGAATTAACGAAGTttttacggag
131393 131407 [GEA], [HIBSCS] [7]
  ArcA-Phosphorylated repressor acnBp Sigma70 -113.0 -209.0 acnB
ccatgcgaatTAACGAAGTTTTTACggagggaaac
131399 131413 [GEA], [HIBSCS] [7]
  ArcA-Phosphorylated repressor acnBp Sigma70 -57.0 -153.0 acnB
gattcagccaCTTTTTTATGTTGCTtttttgtaaa
131455 131469 [GEA], [HIBSCS] [7]
  ArcA-Phosphorylated repressor acnBp Sigma70 -48.0 -144.0 acnB
acttttttatGTTGCTTTTTTGTAAacagattaac
131464 131478 [GEA], [HIBSCS] [7]
  ArcA-Phosphorylated repressor aldAp Sigma70 -157.0 -199.0 aldA
aaagtcgctcGTTACGTTAAAAATTgcccgtttgt
1488026 1488040 [BPP], [HIBSCS] [8]
  ArcA-Phosphorylated repressor aldAp Sigma70 -137.0 -179.0 aldA
aaattgcccgTTTGTGAACCACTTGtttgcaaacg
1488046 1488060 [BPP], [HIBSCS] [8]
  ArcA-Phosphorylated repressor aldAp Sigma70 -5.0 -47.0 aldA
gatgattgatGTTAATTAACAATGTattcaccgaa
1488178 1488192 [BPP], [HIBSCS], [SM] [8], [9]
  ArcA-Phosphorylated repressor aldAp Sigma70 2.0 -41.0 aldA
tgatgttaatTAACAATGTATTCACcgaaaacaaa
1488184 1488198 [AIBSCS], [BPP] [8], [9]
  ArcA-Phosphorylated repressor aldAp Sigma70 13.0 -30.0 aldA
aacaatgtatTCACCGAAAACAAACatataaatca
1488195 1488209 [AIBSCS], [BPP], [SM] [8], [9]
  ArcA-Phosphorylated activator appCp Sigma70 nd nd appC, appB, appX, appA nd nd [GEA] [10]
  ArcA-Phosphorylated repressor arcZp nd -29.0 -29.0 arcZ
aactgattcaTGTAACAAATCATTTaagttttgct
3350541 3350555 [GEA], [HIBSCS] [11]
  ArcA-Phosphorylated repressor betIp Sigma70 -74.0 -101.0 betI, betB, betA
cactgttattGTTACTATTTAAAATcaaattcgta
329428 329442 [BCE], [GEA] [12]
  ArcA-Phosphorylated repressor betIp Sigma70 -6.0 -33.0 betI, betB, betA
tcaataaccgCTTTAATAGATAAACaccgctgatg
329360 329374 [BCE] [12], [13]
  ArcA-Phosphorylated repressor betTp Sigma70 3.0 -40.0 betT
tgtcttaattGTTACGAATTTGATTttaaatagta
329416 329430 [BCE], [GEA] [12], [13]
  ArcA-Phosphorylated repressor betTp Sigma70 15.0 -28.0 betT
tacgaatttgATTTTAAATAGTAACaataacagtg
329428 329442 [BCE], [GEA] [12]
  ArcA-Phosphorylated repressor cadBp Sigma70 -179.0 -254.0 cadB, cadA
ataatttttaTTACATAAATTTAACcagagaatgt
4360278 4360292 [AIBSCS], [GEA] [9]
  ArcA-Phosphorylated activator caiTp Sigma70 -101.0 -207.0 caiT, caiA, caiB, caiC, caiD, caiE
cagagcataaCAAACTGATTATTAAtcaaaattaa
42131 42145 [AIBSCS], [GEA] [9]
  ArcA-Phosphorylated activator caiTp Sigma70 -91.0 -197.0 caiT, caiA, caiB, caiC, caiD, caiE
caaactgattATTAATCAAAATTAAcgaaaaaacg
42121 42135 [AIBSCS], [GEA] [9]
  ArcA-Phosphorylated activator caiTp Sigma70 28.0 -79.0 caiT, caiA, caiB, caiC, caiD, caiE
cgtccacgagGTTAATAATAATTATattaaatgtt
42003 42017 [AIBSCS], [GEA] [9]
  ArcA-Phosphorylated activator caiTp Sigma70 50.0 -57.0 caiT, caiA, caiB, caiC, caiD, caiE
tatattaaatGTTAACAAAAATAAAacaaacggga
41981 41995 [AIBSCS], [GEA] [9]
  ArcA-Phosphorylated repressor citCp1 nd 64.5 -32.5 citC, citD, citE, citF, citX, citG
ttcgttgcaaATCGATAACAacatgcacct
651884 651893 [AIBSCS] [14]
  ArcA-Phosphorylated activator cydAp1 Sigma70 -315.0 -603.0 cydA, cydB
ccctgggtgaGTTAATTATAATATAattataagtt
770848 770862 [AIBSCS], [GEA] [9], [15], [16], [17]
  ArcA-Phosphorylated activator cydAp1 Sigma70 -304.0 -592.0 cydA, cydB
ttaattataaTATAATTATAAGTTAactaaatgtt
770859 770873 [AIBSCS], [GEA] [9], [15], [16], [17]
  ArcA-Phosphorylated activator cydAp1 Sigma70 -293.0 -581.0 cydA, cydB
ataattataaGTTAACTAAATGTTAatattggcgg
770870 770884 [AIBSCS], [BPP], [GEA] [9], [13], [15], [16], [17], [18], [19]
  ArcA-Phosphorylated activator cydAp1 Sigma70 -84.0 -372.0 cydA, cydB
aagttaccttATTGAAACATGATTAacataatttg
771079 771093 [BCE], [GEA], [HIBSCS] [9], [13], [15], [16], [17], [18], [19]
  ArcA-Phosphorylated activator cydAp1 Sigma70 135.0 -154.0 cydA, cydB
ggatcaatttGAGTTTTTATTAACAtgtttgcaac
771297 771311 [AIBSCS], [GEA] [9], [15], [16], [17]
  ArcA-Phosphorylated activator cydAp2 Sigma70 -77.5 -252.0 cydA, cydB
cggtaatttaGCTATAAATTGATCAccgtcgaaaa
771199 771213 [BPP], [GEA], [HIBSCS] [13], [15], [17]
  ArcA-Phosphorylated activator cydAp3 Sigma70 nd nd cydA, cydB nd nd [AIBSCS], [GEA] [15], [17], [20], [21]
  ArcA-Phosphorylated activator cydAp4 Sigma70 nd nd cydA, cydB nd nd [AIBSCS], [GEA] [15], [17], [20], [21]
  ArcA-Phosphorylated activator cydDp Sigma70 nd nd cydD, cydC nd nd [GEA] [17]
  ArcA-Phosphorylated repressor cyoAp Sigma70 -200.0 -243.0 cyoA, cyoB, cyoC, cyoD, cyoE
ataattatttGTTAAATAATTGTTTtatttcacat
451846 451860 [BCE], [GEA] [13], [18], [22], [23]
  ArcA-Phosphorylated repressor dctAp Sigma70 nd nd dctA nd nd [GEA] [24]
  ArcA-Phosphorylated activator dcuCp nd -340.0 -455.0 dcuC
gcttgttcaaGTTAAATATTTCCGCgcatcgatta
656416 656430 [GEA], [HIBSCS] [25]
  ArcA-Phosphorylated activator dpiBp nd -95.5 -346.5 dpiB, dpiA
aggtgcatgtTGTTATCGATttgcaacgaa
651884 651893 [AIBSCS] [14]
  ArcA-Phosphorylated repressor fadBp Sigma70 -29.0 -71.0 fadB, fadA
aatcttttgtTTGCATATTTTTAACacaaaataca
4031035 4031049 [AIBSCS], [BPP], [GEA] [9], [23], [26]
  ArcA-Phosphorylated repressor fadDp Sigma70 -7.0 -68.0 fadD, sroD
ggtatgatgaGTTAATATTATGTTAacggcatgta
1889807 1889821 [AIBSCS], [BPP] [26]
  ArcA-Phosphorylated repressor fadEp nd 15.0 -89.0 fadE
gctttgttgtAATTATATTGTAAACatattgctaa
243385 243399 [AIBSCS], [BPP], [GEA] [26]
  ArcA-Phosphorylated repressor fadHp nd 19.0 -23.0 fadH
tccgaccacaTAACAATTATTTTACatactggaca
3231635 3231649 [GEA], [HIBSCS] [26], [27]
  ArcA-Phosphorylated repressor fadIp Sigma70 -17.0 -59.0 fadI, fadJ
ttggctaaatGTAAAAAAATGGTTAagactatgat
2460521 2460535 [AIBSCS], [BPP], [GEA] [26]
  ArcA-Phosphorylated repressor fadLp Sigma38 -38.0 -139.0 fadL
aaaaagatagAAACATACTTGCAACattccagctg
2461160 2461174 [AIBSCS], [BPP] [26]
  ArcA-Phosphorylated repressor fnrp Sigma70 nd nd fnr nd nd [GEA] [6]
  ArcA-Phosphorylated activator focAp1 Sigma70 -251.0 -278.0 focA, pflB
tataaggttaAATATCGGTAATTTGtatttaataa
954737 954751 [GEA], [HIBSCS] [6], [28], [29], [30], [31]
  ArcA-Phosphorylated activator focAp1 Sigma70 -114.0 -141.0 focA, pflB
tttatttttaTTTGGATAATCAAATatttactccg
954600 954614 [BPP], [GEA], [HIBSCS] [28], [29], [30], [31]
  ArcA-Phosphorylated activator focAp1 Sigma70 -6.0 -33.0 focA, pflB
ataatgctttGTTAGTATCTCGTCGccgacttaat
954492 954506 [GEA], [HIBSCS] [6], [28], [29], [30], [31]
  ArcA-Phosphorylated activator focAp2 Sigma70 5.0 -33.0 focA, pflB
ataatgctttGTTAGTATCTCGTCGccgacttaat
954492 954506 [GEA], [HIBSCS] [6], [28], [29], [30], [31]
  ArcA-Phosphorylated repressor fumAp Sigma70 nd nd fumA, fumC nd nd [GEA] [23], [32]
  ArcA-Phosphorylated activator fumBp Sigma70 nd nd fumB nd nd [GEA] [33]
  ArcA-Phosphorylated repressor fumCp Sigma38 nd nd fumC nd nd [GEA] [32]
  ArcA-Phosphorylated activator gadAp Sigma38 nd nd gadA, gadX nd nd [AIBSCS], [GEA] [22]
  ArcA-Phosphorylated activator gadEp1 Sigma38 nd nd gadE, gadF nd nd [BPP], [GEA] [34]
  ArcA-Phosphorylated activator gadEp3 Sigma70 nd nd gadE, gadF nd nd [BPP], [GEA] [34]
  ArcA-Phosphorylated repressor gatYp Sigma70 nd nd gatY, gatZ, gatA, gatB, gatC, gatD nd nd [AIBSCS], [GEA] [22]
  ArcA-Phosphorylated repressor glcDp Sigma70 -111.0 -166.0 glcD, glcE, glcF, glcG, glcB, glcA
aagtgattatGTTACATCAATTTAAcattgagtta
3128180 3128194 [BPP], [GEA] [35]
  ArcA-Phosphorylated repressor glcDp Sigma70 -104.0 -159.0 glcD, glcE, glcF, glcG, glcB, glcA
tatgttacatCAATTTAACATTGAGttaaccaaga
3128173 3128187 [AIBSCS], [BPP], [GEA] [9], [35]
  ArcA-Phosphorylated repressor glpABCp Sigma70 nd nd glpA, glpB, glpC nd nd [GEA] [36]
  ArcA-Phosphorylated repressor glpDp Sigma70 nd nd glpD nd nd [GEA] [36]
  ArcA-Phosphorylated repressor gltAp1 Sigma70 -47.0 -346.0 gltA
tgacaatcatTCAACAAAGTTGTTAcaaacattac
754807 754821 [BCE], [GEA], [HIBSCS] [13], [17], [22], [37], [38]
  ArcA-Phosphorylated activator grcAp1 Sigma70 -99.0 -173.0 grcA
ttcacacccgCATAAGTTGATGTAAaacaataaaa
2716615 2716629 [GEA], [HIBSCS] [39]
  ArcA-Phosphorylated activator grcAp1 Sigma70 -82.0 -156.0 grcA
tgatgtaaaaCAATAAAATCCATTTgcgaccatac
2716598 2716612 [GEA], [HIBSCS] [39]
  ArcA-Phosphorylated activator hemAp1 Sigma70 nd nd hemA, prfA, prmC nd nd [GEA] [40], [41]
  ArcA-Phosphorylated activator hyaAp Sigma70 -67.0 -222.0 hyaA, hyaB, hyaC, hyaD, hyaE, hyaF
aaaaataggtCCATTTTTATCGCTAaaagataaat
1031910 1031924 [GEA], [HIBSCS] [42], [43]
  ArcA-Phosphorylated activator hyaAp Sigma70 -7.5 -162.5 hyaA, hyaB, hyaC, hyaD, hyaE, hyaF
gtgcaaaagtTTCACTACGCTTTATTAACAATactttctggc
1031966 1031987 [BPP], [GEA], [HIBSCS] [44]
  ArcA-Phosphorylated repressor hybOp1 Sigma70 -57.0 -159.0 hybO, hybA, hybB, hybC, hybD, hybE, hybF, hybG
attatcttgcTTTAATTAATTACACtaatgcttct
3146413 3146427 [GEA], [HIBSCS] [43]
  ArcA-Phosphorylated repressor icdAp1 Sigma70 -3.0 -118.0 icd
caatagggtaGTATTGACAAGCCAAttacaaatca
1194998 1195012 [BPP], [GEA], [HIBSCS] [17], [22], [45], [46]
  ArcA-Phosphorylated repressor icdAp1 Sigma70 16.0 -100.0 icd
aagccaattaCAAATCATTAACAAAaaattgctct
1195016 1195030 [BPP], [GEA], [HIBSCS] [17], [22], [45], [46]
  ArcA-Phosphorylated activator iraMp nd -170.5 -257.0 iraM
ataaaggctaTGTTTTAATTACAGGatgttcagtc
1212253 1212267 [AIBSCS] [47]
  ArcA-Phosphorylated activator iraMp nd -16.5 -103.0 iraM
tataagccatCATTTTAATTAATTTatttttttga
1212099 1212113 [AIBSCS] [47]
  ArcA-Phosphorylated repressor lldPp Sigma70 -18.0 -128.0 lldP, lldR, lldD
gttgccaataCATAACATTTAGTTAaccattcatt
3777264 3777278 [AIBSCS], [BPP], [GEA], [HIBSCS] [9], [13], [15]
  ArcA-Phosphorylated repressor lldPp Sigma70 10.0 -101.0 lldP, lldR, lldD
cattcattgtCATTATCCCTACACAacacaattgg
3777291 3777305 [BPP], [GEA] [9], [13], [15]
  ArcA-Phosphorylated repressor lpdAp Sigma70 -27.0 -222.0 lpd
cgtttgttgtTTAAAAATTGTTAACaattttgtaa
127683 127697 [AIBSCS] [9]
  ArcA-Phosphorylated repressor lpdAp Sigma70 -18.0 -213.0 lpd
tttaaaaattGTTAACAATTTTGTAaaataccgac
127692 127706 [AIBSCS], [BPP], [GEA] [9], [22], [48], [49], [50]
  ArcA-Phosphorylated repressor mdhp1 Sigma70 27.0 -19.0 mdh
catatcttagTTTATCAATATAATAaggagtttag
3384280 3384294 [BCE], [GEA] [13], [22], [37], [51]
  ArcA-Phosphorylated activator moeAp Sigma70 -137.0 -167.0 moeA, moeB
tggttcgccaCTTTTGCTATAAATAtcagaatttt
866524 866538 [BPP], [GEA] [52]
  ArcA-Phosphorylated repressor ndhp Sigma70 -57.0 -150.0 ndh
cttttcagcaACAAAACTTGATTAAcatcaatttt
1165928 1165942 [AIBSCS], [GEA] [9], [53]
  ArcA-Phosphorylated repressor ndhp Sigma70 36.0 -58.0 ndh
gtaacctgttGTTAATTAAGAGCTAtgttaataac
1166020 1166034 [AIBSCS], [GEA] [9], [53]
  ArcA-Phosphorylated repressor ndhp Sigma70 52.0 -42.0 ndh
taagagctatGTTAATAACCATTAAttaacaattg
1166036 1166050 [AIBSCS], [GEA] [9], [53]
  ArcA-Phosphorylated repressor ndhp Sigma70 57.0 -37.0 ndh
gctatgttaaTAACCATTAATTAACaattggttaa
1166041 1166055 [AIBSCS], [GEA] [9], [53]
  ArcA-Phosphorylated repressor ndhp Sigma70 66.0 -28.0 ndh
ataaccattaATTAACAATTGGTTAataaatttaa
1166050 1166064 [AIBSCS], [GEA] [9], [53]
  ArcA-Phosphorylated repressor ndhp Sigma70 68.0 -26.0 ndh
aaccattaatTAACAATTGGTTAATaaatttaagg
1166052 1166066 [AIBSCS], [GEA] [9], [53]
  ArcA-Phosphorylated repressor nuoAp2 Sigma70 -108.0 -198.0 nuoA, nuoB, nuoC, nuoE, nuoF, nuoG, nuoH, nuoI, nuoJ, nuoK, nuoL, nuoM, nuoN
tgctaatggtGTTGATATTATGTAAactaatgtga
2405263 2405277 [BCE], [GEA], [SM] [13], [17], [22], [54]
  ArcA-Phosphorylated repressor ompWp nd 1.5 -28.5 ompW
tgtaggtataTTCGTCACGTTTTTATAAccataacgac
1313983 1314000 [AIBSCS], [BPP], [GEA] [55], [56]
  ArcA-Phosphorylated repressor oppAp Sigma28 nd nd oppA, oppB, oppC, oppD, oppF nd nd [AIBSCS], [GEA] [22]
  ArcA-Phosphorylated repressor ptsGp1 nd -85.0 -188.0 ptsG
tgtgacatatGTTTTGTCAAAATGTgcaacttctc
1157674 1157688 [BPP], [GEA] [57]
  ArcA-Phosphorylated repressor ptsGp1 nd -48.0 -151.0 ptsG
atgatctgaaGTTGAAACGTGATAGccgtcaaaca
1157711 1157725 [BPP], [GEA] [57]
  ArcA-Phosphorylated repressor ptsGp1 nd 2.0 -102.0 ptsG
tattttactcTGTGTAATAAATAAAgggcgcttag
1157760 1157774 [BPP], [GEA] [57]
  ArcA-Phosphorylated repressor puuAp Sigma38 -165.0 -225.0 puuA, puuP
cgataaccggATTGTTCATTATATTttccatgctc
1361126 1361140 [AIBSCS], [GEA] [47]
  ArcA-Phosphorylated repressor puuDp Sigma38 82.0 13.0 puuD, puuR, puuC, puuB, puuE
gagcatggaaAATATAATGAACAATccggttatcg
1361126 1361140 [AIBSCS], [GEA] [47]
  ArcA-Phosphorylated repressor rhaTp Sigma70 -184.0 -225.0 rhaT
gtaagcagttGGTTCATTATAGTTAattaaatgat
4100743 4100757 [AIBSCS], [GEA] [9]
  ArcA-Phosphorylated repressor rhaTp Sigma70 -173.0 -214.0 rhaT
gttcattataGTTAATTAAATGATAttgaaaatga
4100732 4100746 [AIBSCS], [GEA] [9]
  ArcA-Phosphorylated repressor rhaTp Sigma70 -156.0 -197.0 rhaT
aaatgatattGAAAATGATTATCAAtgccgtactt
4100715 4100729 [AIBSCS], [GEA] [9]
  ArcA-Phosphorylated repressor rpoSp Sigma70 -64.0 -631.0 rpoS
agagcaaggaGTTGTGATCAAGCCTgcacaaaatt
2868175 2868189 [BPP], [GEA] [58]
  ArcA-Phosphorylated repressor rpoSp Sigma70 24.0 -544.0 rpoS
tgaacagagtGCTAACAAAATGTTGccgaacaaca
2868088 2868102 [BPP], [GEA] [58]
  ArcA-Phosphorylated repressor rpsJp Sigma70 nd nd rpsJ, rplC, rplD, rplW, rplB, rpsS, rplV, rpsC, rplP, rpmC, rpsQ nd nd [AIBSCS], [GEA] [22]
  ArcA-Phosphorylated activator rutAp Sigma54 -97.0 -112.0 rutA, rutB, rutC, rutD, rutE, rutF, rutG
ctgttttgacCGTTTAGTCCACTTTttaccagata
1074116 1074130 [AIBSCS], [GEA] [22]
  ArcA-Phosphorylated activator sdhCp Sigma70 -211.0 -430.0 sdhC, sdhD, sdhA, sdhB, sucA, sucB, sucC, sucD
tgttacataaGTTAATCTTAGGTGAaataccgact
754740 754754 [GEA], [HIBSCS] [59]
  ArcA-Phosphorylated activator sdhCp Sigma70 -137.0 -356.0 sdhC, sdhD, sdhA, sdhB, sucA, sucB, sucC, sucD
ttgtaacaacTTTGTTGAATGATTGtcaaattaga
754814 754828 [BPP], [GEA] [59]
  ArcA-Phosphorylated repressor sdhCp Sigma70 -32.0 -251.0 sdhC, sdhD, sdhA, sdhB, sucA, sucB, sucC, sucD
atgtaggttaATTGTAATGATTTTGtgaacagcct
754919 754933 [BPP], [GEA], [HIBSCS] [5], [13]
  ArcA-Phosphorylated repressor sdhCp Sigma70 -27.0 -246.0 sdhC, sdhD, sdhA, sdhB, sucA, sucB, sucC, sucD
ggttaattgtAATGATTTTGTGAACagcctatact
754924 754938 [GEA], [HIBSCS] [5], [49], [59], [60]
  ArcA-Phosphorylated repressor sdhCp Sigma70 257.0 37.0 sdhC, sdhD, sdhA, sdhB, sucA, sucB, sucC, sucD
acaaagacctGTTAATCTGGACCTAcagaccatcc
755207 755221 [BPP], [GEA] [59]
  ArcA-Phosphorylated repressor sodAp Sigma70 -38.0 -89.0 sodA
aaagtacggcATTGATAATCATTTTcaatatcatt
4100714 4100728 [BCE] [9], [61]
  ArcA-Phosphorylated repressor sodAp Sigma70 -21.0 -72.0 sodA
atcattttcaATATCATTTAATTAActataatgaa
4100731 4100745 [AIBSCS], [BCE] [9], [61]
  ArcA-Phosphorylated repressor sodAp Sigma70 -10.0 -61.0 sodA
tatcatttaaTTAACTATAATGAACcaactgctta
4100742 4100756 [BCE], [HIBSCS] [61]
  ArcA-Phosphorylated repressor ssbp1 Sigma70 -153.5 -187.0 ssb
ggcgatcacaAACGGTTAATTATGAcacaaattga
4273931 4273945 [BPP], [GEA], [HIBSCS] [62]
  ArcA-Phosphorylated repressor ssbp1 Sigma70 -90.5 -124.0 ssb
attacccggaGTGTTGTGTAACAATgtctggccag
4273994 4274008 [BPP], [GEA], [HIBSCS] [62]
  ArcA-Phosphorylated repressor ssbp1 Sigma70 -50.5 -84.0 ssb
tttcccggaaCCGAGGTCACAACATagtaaaagcg
4274034 4274048 [BPP], [GEA], [HIBSCS] [62]
  ArcA-Phosphorylated repressor ssbp1 Sigma70 -7.5 -41.0 ssb
aatggtacaaTCGCGCGTTTACACTtattcagaac
4274077 4274091 [BPP], [GEA], [HIBSCS] [62]
  ArcA-Phosphorylated repressor ssbp2 Sigma70 -141.5 -187.0 ssb
ggcgatcacaAACGGTTAATTATGAcacaaattga
4273931 4273945 [BPP], [GEA], [HIBSCS] [62]
  ArcA-Phosphorylated repressor ssbp2 Sigma70 -78.5 -124.0 ssb
attacccggaGTGTTGTGTAACAATgtctggccag
4273994 4274008 [BPP], [GEA], [HIBSCS] [62]
  ArcA-Phosphorylated repressor ssbp2 Sigma70 -38.5 -84.0 ssb
tttcccggaaCCGAGGTCACAACATagtaaaagcg
4274034 4274048 [BPP], [GEA], [HIBSCS] [62]
  ArcA-Phosphorylated repressor ssbp2 Sigma70 5.5 -41.0 ssb
aatggtacaaTCGCGCGTTTACACTtattcagaac
4274077 4274091 [BPP], [GEA], [HIBSCS] [62]
  ArcA-Phosphorylated repressor ssbp3 Sigma70 -72.5 -187.0 ssb
ggcgatcacaAACGGTTAATTATGAcacaaattga
4273931 4273945 [BPP], [GEA], [HIBSCS] [62]
  ArcA-Phosphorylated repressor ssbp3 Sigma70 -9.5 -124.0 ssb
attacccggaGTGTTGTGTAACAATgtctggccag
4273994 4274008 [BPP], [GEA], [HIBSCS] [62]
  ArcA-Phosphorylated repressor ssbp3 Sigma70 31.5 -84.0 ssb
tttcccggaaCCGAGGTCACAACATagtaaaagcg
4274034 4274048 [BPP], [GEA], [HIBSCS] [62]
  ArcA-Phosphorylated repressor ssbp3 Sigma70 74.5 -41.0 ssb
aatggtacaaTCGCGCGTTTACACTtattcagaac
4274077 4274091 [BPP], [GEA], [HIBSCS] [62]
  ArcA-Phosphorylated repressor sucAp Sigma38 nd nd sucA, sucB, sucC, sucD nd nd [BPP], [GEA] [13], [23], [63]
  ArcA-Phosphorylated repressor tpxp Sigma70 -22.0 -55.0 tpx
cgtttgctgtGTTATTGACAGTTAGcataaactag
1388859 1388873 [GEA], [HIBSCS] [64]
  ArcA-Phosphorylated activator treBp Sigma70 -237.0 -267.0 treB, treC
ggcgagcgtcGGTAATACGCCGTTAatgaaattcc
4466440 4466454 [AIBSCS], [GEA] [9]
  ArcA-Phosphorylated repressor ubiCp Sigma70 nd nd ubiC, ubiA nd nd [GEA] [65]
  ArcA-Phosphorylated repressor uvrAp Sigma70 -148.5 -213.0 uvrA
gttctgaataAGTGTAAACGCGCGAttgtaccatt
4274077 4274091 [BPP], [GEA], [HIBSCS] [62]
  ArcA-Phosphorylated repressor uvrAp Sigma70 -105.5 -170.0 uvrA
cgcttttactATGTTGTGACCTCGGttccgggaaa
4274034 4274048 [BPP], [GEA], [HIBSCS] [62]
  ArcA-Phosphorylated repressor uvrAp Sigma70 -65.5 -130.0 uvrA
ctggccagacATTGTTACACAACACtccgggtaat
4273994 4274008 [BPP], [GEA], [HIBSCS] [62]
  ArcA-Phosphorylated repressor uvrAp Sigma70 -2.5 -67.0 uvrA
tcaatttgtgTCATAATTAACCGTTtgtgatcgcc
4273931 4273945 [BPP], [GEA], [HIBSCS] [62]
  ArcA-Phosphorylated activator xylRp nd nd nd xylR nd nd [AIBSCS], [GEA] [22]
  ArcA-Phosphorylated activator ybdNp Sigma70 64.5 -53.0 ybdN
acagtgtttaCTTTATAATTAACAGacttatctca
636615 636629 [AIBSCS] [47]
  ArcA-Phosphorylated repressor ydeAp nd 16.0 -58.0 ydeA
aatgcattgtATTCACATCATTAACcgttttaaga
1616963 1616977 [AIBSCS], [GEA] [9]


Alignment and PSSM for ArcA TFBSs    

Aligned TFBS of ArcA   
  Sequence
  TGTTAACAAAAATAAAA
  GGTTAATAATAATTATA
  TATTAATCAAAATTAAC
  TGTTAACAATTTTTAAA
  TTTAAATTTTGACTAAT