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Cra DNA-binding transcriptional dual regulator

Synonyms: Cra-;-D-fructose 1,6-bisphosphate, Cra-β-D-fructose 1,6-bisphosphate, Cra-β-D-fructofuranose 1-phosphate, Cra
Summary:
"Catabolite repressor activator," Cra, which was initially named "Fructose repressor," "FruR," is a dual transcriptional regulator that plays a pleiotropic role to modulate the direction of carbon flow through the different metabolic pathways of energy metabolism, but independently of the CRP regulator [7, 8, 13]. For this reason the Cra regulator is implicated in the expression of a large number of operons that encode enzymes which comprise central pathways of carbon metabolism. Cra acts as an activator of genes encoding gluconeogenic [7, 24, 26], Krebs cycle [27], and glyoxylate shunt [1, 27]enzymes, and the negative effect on genes encoding Entner-Doudoroff pathway [13] and glycolytic enzymes [7, 24].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
Cra Functional   Apo [APPH], [BPP], [GEA], [HIFS] [1], [2], [3], [4], [5], [6], [7], [8], [9]
Cra-β-D-fructofuranose 1-phosphate Non-Functional Allosteric Holo [BPP], [GEA] [7], [8]
Cra-β-D-fructose 1,6-bisphosphate Non-Functional Allosteric Holo nd nd
Cra-;-D-fructose 1,6-bisphosphate Non-Functional Allosteric Holo [BPP], [GEA] [7], [8]
Evolutionary Family: GalR/LacI
Sensing class: Using internal synthesized signals
Connectivity class: Local Regulator
Gene name: cra
  Genome position: 88028-89032
  Length: 1005 bp / 334 aa
Operon name: cra
TU(s) encoding the TF:
Transcription unit        Promoter
cra
fruRp8


Regulon       
Regulated gene(s) aceA, aceB, aceE, aceF, aceK, acnA, acnB, adhE, aroP, betA, betB, betI, betT, crp, crr, csgD, csgE, csgF, csgG, cydA, cydB, cyoA, cyoB, cyoC, cyoD, cyoE, cysG, eda, edd, eno, envC, epd, fbaA, fbaB, fruA, fruB, fruK, gapA, glcC, glk, gpmM, hypF, icd, lpd, manX, manY, manZ, marA, marB, marR, mpl, mtlA, mtlD, mtlR, nirB, nirC, nirD, pck, pdeL, pdhR, pfkA, pgk, poxB, ppc, ppsA,
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Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
carbon compounds (26)
membrane (19)
Transcription related (8)
repressor (8)
Phosphotransferase Systems (PEP-dependent PTS) (7)
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Regulated operon(s) aceBAK, acnB, adhE, aroP, betIBA, betT, crp, csgDEFG, cydAB, cyoABCDE, edd-eda, epd-pgk-fbaA, fbaB, fruBKA, gapA-yeaD, glcC, glk, gpmM-envC-yibQ, hcp-hcr-poxB-ltaE-ybjT, hydN-hypF, icd, manXYZ, marRAB, mpl, mtlADR, nirBDC-cysG, pck, pdeL, pdhR-aceEF-lpd, pfkA, ppc, ppsA, prpBCDE, ptsHI-crr, pykF, pyrG-eno, sgrST-setA, tpiA, ymiC-acnA, zwf
First gene in the operon(s) aceB, acnA, acnB, adhE, aroP, betI, betT, crp, csgD, cydA, cyoA, edd, eno, epd, fbaB, fruB, gapA, glcC, glk, gpmM, hypF, icd, manX, marR, mpl, mtlA, nirB, pck, pdhR, pfkA, poxB, ppc, ppsA, prpB, ptsH, pykF, sgrS, tpiA, pdeL, zwf
Simple and complex regulons AcrR,CRP,CpxR,Cra,Fis,MarA,MarR,Rob,SoxS
ArcA,BetI,Cra
ArcA,CRP,Cra,CusR,FNR,Fis,Fur,GadE,HprR,PdhR
ArcA,CRP,Cra,FNR,MarA,Rob,SoxS
ArcA,CRP,Cra,Fis
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Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[Cra,+](14)
[Cra,-](34)


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 Growth Conditions Evidence (Confirmed, Strong, Weak) References
  Cra activator aceBp Sigma70 -166.5 -242.5 aceB, aceA, aceK
tgatagtcgaTCGTTAAGCGATTCAGCAccttacctca
 4215227 4215244 nd [BPP], [CV(CHIP-SV/SM)], [GEA], [SM] [1], [8], [10]
  Cra activator acnAp2 Sigma70 nd nd acnA
nd
 nd nd nd [GEA] [11]
  Cra repressor acnBp Sigma70 nd nd acnB
nd
 nd nd nd [GEA] [11]
  Cra repressor adhEp1 Sigma38, Sigma70 36.5 -256.5 adhE
cgaaaagcgaTGCTGAAAGGTGTCAGCtttgcaaaaa
 1298370 1298386 nd [BCE], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [GEA], [ICWHO], [SM] [4], [12], [13]
  Cra activator aroPp1 Sigma70 -177.5 -297.5 aroP
taaaaatccgAATTGAACCGATTCACTTaccaattttg
 121840 121857 nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [13], [14]
  Cra activator aroPp2 Sigma70 -198.5 -297.5 aroP
taaaaatccgAATTGAACCGATTCACTTaccaattttg
 121840 121857 nd [AIBSCS], [CV(GEA/ROMA)], [GEA], [ICWHO] [13], [14]
  Cra activator betIp Sigma70 nd nd betI, betB, betA
nd
 nd nd nd [GEA] [10]
  Cra activator betTp Sigma70 nd nd betT
nd
 nd nd nd [GEA] [10]
  Cra activator crpp1 Sigma70 -45.5 -212.5 crp
cctgggtcatGCTGAAGCGAGACACCAggagacacaa
 3485900 3485916 nd [BPP], [CV(CHIP-SV/SM)], [GEA], [SM] [15]
  Cra activator csgDp1 Sigma38, Sigma70 -563.5 -711.5 csgD, csgE, csgF, csgG
catttaagaaATTAAATCATTTCAACTTggttgttaac
 1103899 1103916 nd [AIBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [16]
  Cra activator csgDp1 Sigma38, Sigma70 -227.5 -375.5 csgD, csgE, csgF, csgG
tgtggagaaaAAACAAGAACGTTTTACAtgacgaaagg
 1103563 1103580 nd [AIBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [GEA], [SM] [16]
  Cra activator csgDp1 Sigma38, Sigma70 -196.5 -344.5 csgD, csgE, csgF, csgG
cgaaaggactACACCGAAATATTTTTTAtatgcattat
 1103532 1103549 nd [AIBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [GEA], [SM] [16]
  Cra activator csgDp1 Sigma38, Sigma70 46.5 -102.5 csgD, csgE, csgF, csgG
tacccatttaGGGCTGATTTATTACTACacacagcagt
 1103290 1103307 nd [AIBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [GEA], [SM] [16]
  Cra activator cydAp5 Sigma70 -134.5 -224.5 cydA, cydB
cgtcgaaaaaTGCAAATTTGCTTCAACAaaaacctgtt
 771225 771242 nd [AIBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [17]
  Cra activator cydAp5 Sigma70 -105.5 -195.5 cydA, cydB
aaacctgtttATTGTAAGGATTTTGCGGcgtaatatat
 771254 771271 nd [AIBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [17]
  Cra repressor cyoAp Sigma70 -268.5 -311.5 cyoA, cyoB, cyoC, cyoD, cyoE
aattctatttTTCTTACACGATTCAGCTaatgagtctt
 451913 451930 nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [14]
  Cra repressor eddp1 Sigma70 4.5 -105.5 edd, eda
ttattacactGACTGAAACGTTTTTGCCctatgagctc
 1934701 1934718 nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [GEA], [SM] [7]
  Cra repressor enop1 nd -205.5 -938.5 eno
gacgattataTTTGTAAACGATTCAGCTtaaactgccc
 2908871 2908888 nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [18]
  Cra repressor enop1 nd -8.5 -741.5 eno
cgtcaacatcAAACTGATCGATTCACAAgatgttgaaa
 2908674 2908691 nd [BPP], [GEA] [18]
  Cra repressor enop2 nd -177.5 -938.5 eno
gacgattataTTTGTAAACGATTCAGCTtaaactgccc
 2908871 2908888 nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [18]
  Cra repressor enop2 nd 20.5 -741.5 eno
cgtcaacatcAAACTGATCGATTCACAAgatgttgaaa
 2908674 2908691 nd [BPP], [GEA] [18]
  Cra repressor enop3 nd -33.5 -938.5 eno
gacgattataTTTGTAAACGATTCAGCTtaaactgccc
 2908871 2908888 nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [18]
  Cra repressor enop3 nd 164.5 -741.5 eno
cgtcaacatcAAACTGATCGATTCACAAgatgttgaaa
 2908674 2908691 nd [BPP], [GEA] [18]
  Cra repressor epdp Sigma70, Sigma38 3.5 -129.5 epd, pgk, fbaA
cgcttatcctAGCTGAAGCGTTTCAGTCgattaaatgt
 3073812 3073829 nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [GEA], [SM] [7]
  Cra repressor fbaBp Sigma38 -35.5 -138.5 fbaB
acattttttcTGATGAATCGAGCCAACAgaaaacgctg
 2178694 2178711 nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [14]
  Cra repressor fruBp Sigma70 7.5 -95.5 fruB, fruK, fruA
gtattatgctTTCTTGAAACGTTTCAGCgcgatcttgt
 2263582 2263599 nd [AIBSCS], [CV(GEA/ROMA)], [GEA], [NAS] [8], [14]
  Cra repressor fruBp Sigma70 73.5 -29.5 fruB, fruK, fruA
ttttctcataGAGGCTGAATCGTTTCAAttcagcaaga
 2263516 2263533 nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [14]
  Cra repressor gapAp1 Sigma70, Sigma38 -725.5 -761.5 gapA
tggaataagtTGCTGAATCGTTTTTTCAaccgttgatt
 1862001 1862018 nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [18]
  Cra repressor gapAp1 Sigma70, Sigma38 -43.5 -79.5 gapA
ttgtcgcaatGATTGACACGATTCCGCTtgacgctgcg
 1862683 1862700 nd [AIBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [18]
  Cra repressor gapAp2 Sigma32 -608.5 -761.5 gapA, yeaD
tggaataagtTGCTGAATCGTTTTTTCAaccgttgatt
 1862001 1862018 nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [18]
  Cra repressor gapAp2 Sigma32 74.5 -79.5 gapA, yeaD
ttgtcgcaatGATTGACACGATTCCGCTtgacgctgcg
 1862683 1862700 nd [AIBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [18]
  Cra repressor gapAp3 Sigma70 -587.5 -761.5 gapA
tggaataagtTGCTGAATCGTTTTTTCAaccgttgatt
 1862001 1862018 nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [18]
  Cra repressor gapAp3 Sigma70 95.5 -79.5 gapA
ttgtcgcaatGATTGACACGATTCCGCTtgacgctgcg
 1862683 1862700 nd [AIBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [18]
  Cra repressor gapAp4 Sigma70 -516.5 -761.5 gapA
tggaataagtTGCTGAATCGTTTTTTCAaccgttgatt
 1862001 1862018 nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [18]
  Cra repressor gapAp4 Sigma70 166.5 -79.5 gapA
ttgtcgcaatGATTGACACGATTCCGCTtgacgctgcg
 1862683 1862700 nd [AIBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [18]
  Cra repressor glcCp Sigma70 -4.5 -70.5 glcC
aattgatgtaACATAATCACTTACGTGAtgtgcgtgtt
 3128193 3128210 nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [14]
  Cra repressor glkp Sigma70, Sigma38 -91.5 -126.5 glk
ctgcaattggTGCTGAAACGATAAAGTAattgtgtgac
 2509544 2509561 nd [AIBSCS], [APIORCISFBSCS], [CV(GEA/ROMA)], [GEA] [14], [19]
  Cra repressor gpmMp nd -31.5 -56.5 gpmM, envC, yibQ
cttcagaggcTATTTTATCGATTCAGCTgtagtaaaat
 3785195 3785212 nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [14]
  Cra repressor hypFp2 Sigma70 -84.5 -673.5 hypF
ctggagaattTGATGAACCGTTTCATCAttgctgacgc
 2838090 2838107 nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [18]
  Cra repressor hypFp3 Sigma70 7.5 -673.5 hypF
ctggagaattTGATGAACCGTTTCATCAttgctgacgc
 2838090 2838107 nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [18]
  Cra activator icdAp2 Sigma70 -76.5 -238.5 icd
gaacgttgcgAGCTGAATCGCTTAACCTggtgatttct
 1194876 1194893 nd [BPP] [20]
  Cra repressor manXp Sigma70 40.5 -75.5 manX, manY, manZ
tgtagcccttATCTGAATCGATTCGATtgtggacgac
 1901965 1901981 nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [13]
  Cra repressor marRp Sigma70 -72.5 -99.5 marR, marA, marB
attgaacaaaACTTGAACCGATTTAGCAaaacgtggca
 1619012 1619029 nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [14]
  Cra repressor mplp1 Sigma38, Sigma70 -36.5 -93.5 mpl
tgttgcgctcAGGTGAATCGCGCCAGCAaattacggat
 4455683 4455700 nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [14]
  Cra repressor mtlAp Sigma70 -22.5 -115.5 mtlA, mtlD, mtlR
gtcgactggaCAGTTAACCGATTCAGTGccagatttcg
 3772157 3772174 nd [BPP], [GEA] [7]
  Cra repressor nirBp Sigma70 -15.5 -39.5 nirB, nirD, nirC, cysG
taagcggggtTGCTGAATCGTTAAGGTAggcggtaata
 3493963 3493980 nd [APIORCISFBSCS], [BCE], [CV(GEA/ROMA)], [GEA] [21], [22]
  Cra activator pckp Sigma70 -139.5 -278.5 pck
aaagttagcgTGGTGAATCGATACTTTAccggttgaat
 3532531 3532548 nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [GEA], [SM] [7]
  Cra repressor pdeLp1 Sigma70 -159.5 -491.5 pdeL
ggttatcattTGCTGAATGGATTCAGTCttaatgagtg
 331871 331888 nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [18]
  Cra repressor pdeLp1 Sigma70 -13.5 -345.5 pdeL
cagttgatctGGATTGTTAAATTCATATaatgcgcctt
 332017 332034 nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [18]
  Cra repressor pdhRp Sigma70, Sigma38 -185.5 -243.5 pdhR, aceE, aceF, lpd
caaaattggtAAGTGAATCGGTTCAATTcggattttta
 121840 121857 nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [13], [14]
  Cra repressor pfkAp2 Sigma70, Sigma38 -35.5 -113.5 pfkA
atttggcctgACCTGAATCAATTCAGCAggaagtgatt
 4107430 4107447 nd [BPP] [5]
  Cra activator poxBp Sigma38, Sigma70 nd nd poxB
nd
 nd nd nd [GEA] [10]
  Cra repressor ppcp nd -46.5 -138.5 ppc
tttattcgttTGCTGAAGCGATTTCGCAgcatttgacg
 4153228 4153245 nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [14]
  Cra activator ppsp Sigma70 -45.5 -94.5 ppsA
aaaatatattTGCTTGAACGATTCACCgtttttttca
 1787199 1787215 nd [AIBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA], [ICWHO] [8], [10], [13], [14]
  Cra repressor prpBp Sigma54 -101.5 -137.5 prpB, prpC, prpD, prpE
ctgaaacgttAACTGAAACGCATATTTGcggattagtt
 348536 348553 nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [14]
  Cra repressor ptsHp1 nd -55.5 -211.5 ptsH, ptsI, crr
gaaaagccaaAGCTGAATCGATTTTATGatttggttca
 2533544 2533561 nd [AIBSCS], [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [14], [23]
  Cra activator ptsHp2 Sigma70 -48.5 -211.5 ptsH, ptsI, crr
gaaaagccaaAGCTGAATCGATTTTATGatttggttca
 2533544 2533561 nd [AIBSCS], [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [14], [23]
  Cra repressor pykFp Sigma70 18.5 -213.5 pykF
gccaattgacTCTTGAATGGTTTCAGCActttggactg
 1755476 1755493 nd [BCE], [SM] [24]
  Cra repressor sgrSp Sigma70, Sigma38 -332.5 -332.5 sgrS, sgrT, setA
tgcaccagttGATCGATACGATCCTGCTccagcaggtc
 77026 77043 nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [14]
  Cra repressor tpiAp2 Sigma70, Sigma38 -91.5 -153.5 tpiA
tgaccttcgcTGTTGAACCGATTAAGCTggcgctatct
 4111652 4111669 nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [14]
  Cra repressor zwfp Sigma70 -35.5 -97.5 zwf
gggtggataaGCGTTTACAGTTTTCGCAagctcgtaaa
 1936403 1936420 nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [14]



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 (Confirmed, Strong, Weak) References
  Cra activator thrA gene -257.5
atagcagcttCTGAACTGGTTACCTgccgtgagta
72 87 79.5 [1] [25]
  Cra activator thrA gene -206.5
acttaggtcaCTAAATACTTTAACCaatataggca
123 138 130.5 [1] [25]
  Cra activator thrA gene -140.5
cacaacatccATGAAACGCATTAGCaccaccatta
189 204 196.5 [1] [25]
  Cra activator thrA gene 46.5
gtggcaaatgCAGAACGTTTTCTGCgtgttgccga
376 391 383.5 [1] [25]
  Cra repressor thrB gene -702.5
cacctcgtcgATGGATTACTACCATcagttgcgtt
2091 2106 2098.5 [2] [25]
  Cra repressor thrB gene -600.5
tgagaacctgCAAAATCTGCTCAATgcaggtgatg
2193 2208 2200.5 [2] [25]
  Cra repressor thrB gene -578.5
aatgcaggtgATGAATTGATGAAGTtctccggcat
2215 2230 2222.5 [2] [25]
  Cra repressor thrB gene -570.5
tgatgaattgATGAAGTTCTCCGGCattctttctg
2223 2238 2230.5 [2] [25]
  Cra repressor thrB gene -548.5
ggcattctttCTGGTTCGCTTTCTTatatcttcgg
2245 2260 2252.5 [2] [25]
  Cra repressor thrB gene -475.5
cgctggcgcgGGAAATGGGTTATACcgaaccggac
2318 2333 2325.5 [2] [25]
  Cra repressor thrB gene -461.5
atgggttataCCGAACCGGACCCGCgagatgatct
2332 2347 2339.5 [2] [25]
  Cra repressor thrB gene -144.5
gttcaaagtgAAAAATGGCGAAAACgccctggcct
2649 2664 2656.5 [2] [25]
  Cra repressor thrB gene 1.5
agttaggagtCTGACATGGTTAAAGtttatgcccc
2795 2810 2802.5 [2] [25]
  Cra activator thrC gene -251.5
cgcgaagctgATGAAAGATGTTATCgctgaaccct
3475 3490 3482.5 [1] [25]
  Cra activator thrC gene -235.5
gatgttatcgCTGAACCCTACCGTGaacggttact
3491 3506 3498.5 [1] [25]
  Cra activator thrC gene -223.5
gaaccctaccGTGAACGGTTACTGCcaggcttccg
3503 3518 3510.5 [1] [25]
  Cra repressor nhaA gene -408.5
tatcgctctcTTTAACCCATTTTGTtttatcgatt
17073 17088 17080.5 [2] [25]
  Cra repressor nhaA gene -394.5
acccattttgTTTTATCGATTCTAAtcctgaagac
17087 17102 17094.5 [2] [25]
  Cra repressor nhaA gene -352.5
atttttgtggCGTAATTTTTTAATGatttaattat
17129 17144 17136.5 [2] [25]
  Cra repressor nhaA gene -336.5
tttttaatgaTTTAATTATTTAACTttaatttatc
17145 17160 17152.5 [2] [25]
  Cra repressor nhaA gene -318.5
tttaactttaATTTATCTCTTCATCgcaattattg
17163 17178 17170.5 [2] [25]
  Cra repressor nhaA gene -285.5
tgacgacaagCTGGATTATTTTTGAaatattggcc
17196 17211 17203.5 [2] [25]
  Cra repressor nhaA gene -38.5
ttcgtgcgggGTAAAATAGTAAAAAcgatctattc
17443 17458 17450.5 [2] [25]
  Cra repressor nhaA gene -29.5
ggtaaaatagTAAAAACGATCTATTcacctgaaag
17452 17467 17459.5 [2] [25]
  Cra repressor nhaA gene 15.5
agtgaaacatCTGCATCGATTCTTTagcagtgatg
17497 17512 17504.5 [2] [25]
  Cra repressor nhaA gene 109.5
ggcgcaaccaGTGGATGGTATCACGactttctgga
17591 17606 17598.5 [2] [25]
  Cra activator fkpB gene -634.5
gccggtgacgGTGAAAAACGTAAGTttgcctgatg
25184 25199 25191.5 [2] [25]
  Cra activator fkpB gene -533.5
ctgggcagcaAATACCTGATCCTCCagaactttgc
25285 25300 25292.5 [2] [25]
  Cra activator fkpB gene -503.5
tttgctctggGGGATACGGTCCCGCtgttcccgtc
25315 25330 25322.5 [2] [25]
  Cra repressor dapB gene 114.5
gggcgctgcgCTGGAGCGTGAAGGAtcttctttac
28481 28496 28488.5 [2] [25]
  Cra activator carA gene -150.5
cacaaaataaTATAAAAAATCCCGCcattaagttg
29493 29508 29500.5 [1] [25]
  Cra activator carA gene -69.5
cgtcggtaagCAGATTTGCATTGATttacgtcatc
29574 29589 29581.5 [1] [25]
  Cra activator carA gene 1.5
tctctggaggGTGTTTTGATTAAGTcagcgctatt
29645 29660 29652.5 [1] [25]
  Cra activator carA gene 155.5
cctattctcgTCAAATCGTTACTCTtacttatccc
29799 29814 29806.5 [1] [25]
  Cra activator leuB gene -589.5
ccccgaacgaGAGGTCAGATTCAGCtggatttggt
82540 82555 82547.5 [1] [25]
  Cra activator leuB gene -632.5
atagattctgGTGTCATGATTTCGTagttttcgcg
82583 82598 82590.5 [1] [25]
  Cra activator leuA gene -137.5
ccgcgcaaagAAGATGCGTTTAGTAgtagtagacc
83659 83674 83666.5 [1] [25]
  Cra activator leuA gene -155.5
tttagtagtaGTAGACCGATAAAGCgaacgatgtg
83677 83692 83684.5 [1] [25]
  Cra activator leuA gene -200.5
tcagctccagATGAATGCGATATGCttttagagtt
83722 83737 83729.5 [1] [25]
  Cra activator leuA gene -285.5
agcgtgagttCTGCATCCGTAAAATtagctaattg
83807 83822 83814.5 [1] [25]
  Cra activator leuA gene -354.5
tgcttaactaCCGACGCTTTTCATCggttgacata
83876 83891 83883.5 [1] [25]
  Cra activator leuA gene -371.5
ttttcatcggTTGACATATTTCAGCataaattttt
83893 83908 83900.5 [1] [25]
  Cra repressor ilvH gene -634.5
tcgtcagtgcCTGAAATATGACACTcacagtgaaa
86715 86730 86722.5 [2] [25]
  Cra repressor ilvH gene -615.5
gacactcacaGTGAAAAGATTAAACcgcaggcggt
86734 86749 86741.5 [2] [25]
  Cra repressor ilvH gene -482.5
aaccgcgtcgCTGGATCAATTCCGGtggcctcggc
86867 86882 86874.5 [2] [25]
  Cra activator murF gene -144.5
gaaggccgtgCTGAAGCGGTGACTTgcgccgttat
94498 94513 94505.5 [1] [25]
  Cra activator murF gene -60.5
gattaccagaTTGTTGGCAATCAGCgtctggacta
94582 94597 94589.5 [1] [25]
  Cra activator secM gene -679.5
tggtttttcgCTGGATTTCACCATCgattttaacc
107018 107033 107025.5 [2]
[1] 		[25]
  Cra activator secM gene -662.5
tcaccatcgaTTTTAACCATCCGGCtattgattcc
107035 107050 107042.5 [2]
[1] 		[25]
  Cra activator secM gene -606.5
aacttctccgCTGATGCGTTTATGCgccagatcag
107091 107106 107098.5 [2]
[1] 		[25]
  Cra activator secM gene -408.5
gatgcgatcgGTGACTTGTTCATGTgtggtcacaa
107289 107304 107296.5 [2]
[1] 		[25]
  Cra activator secM gene -360.5
tttaccgcttATAAATCCGGTCATGcactgaataa
107337 107352 107344.5 [2]
[1] 		[25]
  Cra activator secM gene -102.5
acgctgttttCTTAAGCACTTTTCCgcacaactta
107595 107610 107602.5 [1] [25]
  Cra activator secM gene -51.5
ggactgcaggCTTTAATGATAAGATttgtgcgcta
107646 107661 107653.5 [2] [25]
  Cra activator secM gene 39.5
gcgacagtttGGTAAACGCTACTTCtggccgcatc
107737 107752 107744.5 [2]
[1] 		[25]
  Cra repressor aceF gene -259.5
taccgactatATGAAACTGTTCGCTgagcaggtcc
125428 125443 125435.5 [2] [25]
  Cra repressor aceF gene 139.5
gcctctatggAAGTTCCGTCTCCGCaggcgggtat
125827 125842 125834.5 [2] [25]
  Cra activator acnB gene -170.5
tctagaccatCCTTAACGATTCAGCcactttttta
131437 131452 131444.5 [1] [25]
  Cra activator acnB gene -51.5
tgctgtctcaCAGGAGCGTGAAGAGaatcgcctgc
131556 131571 131563.5 [1] [25]
  Cra activator acnB gene 9.5
aaccgtcgtgCTAGAAGAATACCGTaagcacgtag
131617 131632 131624.5 [1] [25]
  Cra activator acnB gene 141.5
agaattcctgTTAGATCTGTTAACCaaccgtgttc
131749 131764 131756.5 [1] [25]
  Cra repressor gcd gene -637.5
tcccggtagaATTTATCGGTTTCTCgatcccggat
141855 141870 141862.5 [2] [25]
  Cra repressor gcd gene -645.5
gaatttatcgGTTTCTCGATCCCGGatgagtttgt
141863 141878 141870.5 [2] [25]
  Cra repressor gcd gene -723.5
ccgtatatcgGCAAAGTGATTCTGCtggacgagta
141941 141956 141948.5 [2] [25]
  Cra repressor panD gene 69.5
gtcaatggcgCAAGAACCTTCATAGtgcaggtccg
146617 146632 146624.5 [2] [25]
  Cra repressor panD gene -142.5
gcgtaccgcgCCGAAGCGTGCCATGtatcgcctgt
146829 146844 146836.5 [2] [25]
  Cra repressor fhuD gene -698.5
atccgctgtcGTTAACCTTTCCTGCcgggaaagtg
169869 169884 169876.5 [2] [25]
  Cra repressor fhuD gene -667.5
agtgaccggtCTGATTGGTCACAACggttctggta
169900 169915 169907.5 [2] [25]
  Cra repressor fhuD gene -645.5
aacggttctgGTAAATCCACTCTGCtcaaaatgct
169922 169937 169929.5 [2] [25]
  Cra repressor fhuD gene -391.5
agctatctcgCTGGTTGGCTTAAAAccgctggcgc
170176 170191 170183.5 [2] [25]
  Cra repressor skp gene 29.5
tattagctgcAGGTCTCGGTTTAGCactggcaact
200504 200519 200511.5 [2] [25]
  Cra repressor yaeQ gene -696.5
ggctgaaggtGAGAATGGCGTAAGTtttgtctggc
213587 213602 213594.5 [2] [25]
  Cra repressor yaeQ gene -231.5
cccagcgcgtCCGGAACGTATCCTAagtctccgct
214052 214067 214059.5 [2] [25]
  Cra repressor yaeP gene 65.5
cccagcgcgtCCGGAACGTATCCTAagtctccgct
214052 214067 214059.5 [2] [25]
  Cra activator mltD gene 83.5
tgaccagctgCAGAAAGGCTCTGTGcgtgctgttg
233864 233879 233871.5 [2] [25]
  Cra activator mltD gene 13.5
cagaggcgagTAATATCGCTTTTGCcttcatgtgt
233934 233949 233941.5 [2] [25]
  Cra repressor rnhA gene -666.5
caacaaggtgAAGCAACAATTCAGCgcattgtacg
236661 236676 236668.5 [2]
[1] 		[25]
  Cra activator ykfM gene 136.5
ttctccaatcATAAAATATTTCCGTggagcatttt
238592 238607 238599.5 [1] [25]
  Cra activator ykfM gene 123.5
aaatatttccGTGGAGCATTTTATTattgaatata
238605 238620 238612.5 [1] [25]
  Cra activator fadE gene -231.5
tacatttatgCTGAAGGATATCCTCatgtaccagg
243527 243542 243534.5 [2] [25]
  Cra activator gmhA gene -8.5
tacatttatgCTGAAGGATATCCTCatgtaccagg
243527 243542 243534.5 [2] [25]
  Cra activator fadE gene -325.5
gacgccaataTTCACGCCATTCAGCgcgcggcggt
243621 243636 243628.5 [2] [25]
  Cra activator gmhA gene 85.5
gacgccaataTTCACGCCATTCAGCgcgcggcggt
243621 243636 243628.5 [2] [25]
  Cra repressor yafN gene 25.5
attctcgctgAAAAATCGGTCAATAtcactgagtt
252023 252038 252030.5 [2] [25]
  Cra repressor yafN gene 64.5
aaaaacccagCTAAATACTTTATTGatcaaccggt
252062 252077 252069.5 [2] [25]
  Cra repressor yafN gene 71.5
cagctaaataCTTTATTGATCAACCggttgcggtt
252069 252084 252076.5 [2] [25]
  Cra activator paoA gene -400.5
aggtgtataaCATAATGGTACAAGCagggtagata
302966 302981 302973.5 [1] [25]
  Cra activator paoA gene -557.5
cgtagcccggTGGATATGTTTAATGcagcgtgtgg
303123 303138 303130.5 [1] [25]
  Cra activator paoA gene -630.5
gctcgcgtaaTTTTCTCAATCCACCgtatattttt
303196 303211 303203.5 [1] [25]
  Cra activator codB gene 15.5
cgtgtcgcaaGATAACAACTTTAGCcaggggccag
354930 354945 354937.5 [1] [25]
  Cra activator codB gene 54.5
gcagtcggcgCGGAAAGGGGTATTGgcattgacgt
354969 354984 354976.5 [1] [25]
  Cra activator codB gene 134.5
gcggcactctCGGAACCGGTCTTAGctatcatgat
355049 355064 355056.5 [1] [25]
  Cra repressor ddlA gene -183.5
gaacgggaagCTAATTTATTCCTGGcttaaatggc
401099 401114 401106.5 [2] [25]
  Cra repressor ddlA gene -313.5
attttgtgtgGGTAATTATTTAAATaagagaaacg
401229 401244 401236.5 [2] [25]
  Cra repressor ddlA gene -330.5
atttaaataaGAGAAACGTTTCGCTggtaatcaaa
401246 401261 401253.5 [2] [25]
  Cra repressor ddlA gene -609.5
accaacagcgGTTGATTGATCAGGTagagggggcg
401525 401540 401532.5 [2] [25]
  Cra repressor aroL gene -98.5
tcactttaagTGGAATTTTTTCTTTacaatcgaaa
406299 406314 406306.5 [1] [25]
  Cra repressor aroL gene -78.5
tctttacaatCGAAATTGTACTAGTttgatggtat
406319 406334 406326.5 [1] [25]
  Cra repressor aroL gene 73.5
atggcccttgCCGATTCGCTTAACCgtcggtttgt
406471 406486 406478.5 [1] [25]
  Cra repressor aroL gene 165.5
aagggaagagTGGGCGGGATTTCGCgccagagaaa
406563 406578 406570.5 [1] [25]
  Cra activator cyoE gene -110.5
aagacaaacgCCGTCATGTTCCAGCcttcatctga
447808 447823 447815.5 [1] [25]
  Cra activator cyoE gene -236.5
gcagctcctgTCATCACCATCCAGAacggaatcac
447934 447949 447941.5 [1] [25]
  Cra activator cyoE gene -247.5
catcaccatcCAGAACGGAATCACCgtcagaatga
447945 447960 447952.5 [1] [25]
  Cra activator cyoA gene 138.5
caacatcaggCCAAATGCCGTCAGTatcagtgaac
451464 451479 451471.5 [1] [25]
  Cra activator cyoA gene -62.5
gggcattttaCGGGAAGGTTACATTactgtaaaca
451665 451680 451672.5 [1] [25]
  Cra activator cyoA gene -198.5
aaggggagtgCTGAAGGAGTCTGGGcgggcaattg
451801 451816 451808.5 [1] [25]
  Cra activator cyoA gene -234.5
tataaccaatGTGAAATAAAACAATtatttaacaa
451837 451852 451844.5 [1] [25]
  Cra activator cyoA gene -311.5
gactcattagCTGAATCGTGTAAGAaaaatagaat
451914 451929 451921.5 [1] [25]
  Cra activator cyoA gene -338.5
aatagaatttATAAATGGCGCCAATaatttccaaa
451941 451956 451948.5 [1] [25]
  Cra activator ampG gene -161.5
tgttggaggcCTGGAACGCACCTTCaacgttgtag
453699 453714 453706.5 [2] [25]
  Cra activator ampG gene -172.5
tggaacgcacCTTCAACGTTGTAGCtggcacgata
453710 453725 453717.5 [2] [25]
  Cra activator ampG gene -210.5
tttggtcattTTGTTGCCATTCTGCgcggtagcga
453748 453763 453755.5 [2] [25]
  Cra activator ffs gene -38.5
ttagccggggCAGCAGTGATAATGCgcctgcgcgt
476402 476417 476409.5 [2] [25]
  Cra activator ffs gene 113.5
tggcagggccCCCACCCATTTCTGCctcccaccgt
476554 476569 476561.5 [2] [25]
  Cra activator hha gene 98.5
tcattatctgATAATTCGTATTTATttttctcgat
480202 480217 480209.5 [2] [25]
  Cra activator hha gene 75.5
atttttctcgATAACACGCTCCAGCgtgtcaattg
480225 480240 480232.5 [2] [25]
  Cra activator hha gene 67.5
cgataacacgCTCCAGCGTGTCAATtgtctggcaa
480233 480248 480240.5 [2] [25]
  Cra activator hha gene -21.5
ctacctatggTTGTAATAATTCTAAcaagataaac
480322 480337 480329.5 [2] [25]
  Cra activator hha gene -152.5
tactgaacaaCATAAAGGTGTCATCcagatattcg
480453 480468 480460.5 [2] [25]
  Cra activator hha gene -194.5
gctcaatgagCTTATTGTCTTCATTatacttaatt
480495 480510 480502.5 [2] [25]
  Cra activator hha gene -248.5
tcgcaatatgCTCAATCAGTTCATTcaactggagg
480549 480564 480556.5 [2] [25]
  Cra activator hha gene -286.5
atcgccgaggTTGGGTCGTTTACCCagccatgatt
480587 480602 480594.5 [2] [25]
  Cra activator hha gene -558.5
acaattaggaAGGAAGCGGGACAGGactcactttt
480859 480874 480866.5 [2]
[1] 		[25]
  Cra activator hha gene