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Synonyms: CsgD |
Summary:
The protein CsgD, for "Curlin subunit gene D," is a transcriptional regulator [6]that regulates a number of genes involved in the Curli assembly, transport, and structural components [6, 7] which are important for biofilm formation [1] In addition, it also regulates genes related to cell surface-associated structures [1, 4, 8] It may also have the capability to respond to starvation and high cell density [1]and positively controls σS expression [5, 9] In general the environmental conditions, such as low osmolarity, low growth temperature (<32°C), and low growth, affect the expression of csgD and the production of the biofilm and cellulose [8, 10, 11] Since csgD is induced during the mid-exponential phase of growth and the CsgD-dependent activation of csg genes is detected in the stationary phase, it has been suggested that CsgD is posttranscriptionally activated in the stationary phase [1] CsgD might activate transcription through two different mechanisms, as suggested by the different locations of its binding sites in the regulatory regions of the genes it activates. Read more > |
Transcription factor | ![]() ![]() |
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TF conformation(s): |
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Evolutionary Family: | LuxR/UhpA | ||||||||||||
Connectivity class: | Local Regulator | ||||||||||||
Gene name: | csgD | ||||||||||||
Genome position: | 1102546-1103196 | ||||||||||||
Length: | 651 bp / 216 aa | ||||||||||||
Operon name: | csgDEFG | ||||||||||||
TU(s) encoding the TF: |
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Regulon |
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Regulated gene(s) | csgA, csgB, csgC, csgD, csgE, csgF, csgG, dgcC, flgM, flgN, fliA, fliE, fliF, fliG, fliH, fliI, fliJ, fliK, fliZ, iraP, nlpA, pepD, tcyJ, ubiT, wrbA, yccJ, yccT, yhbS | ||||||
Multifun term(s) of regulated gene(s) |
MultiFun Term (List of genes associated to the multifun term)
flagella (10)
motility, chemotaxis, energytaxis (aerotaxis, redoxtaxis etc) (8)
flagellum (5)
fimbri, pili (3)
Transcription related (3)
Read more >
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Regulated operon(s) | csgBAC, csgDEFG, dgcC, flgAMN, fliAZ-tcyJ, fliE, fliFGHIJK, iraP, nlpA, pepD, ubiT-yhbS, wrbA-yccJ, yccT | ||||||
First gene in the operon(s) | dgcC, csgB, csgD, flgM, fliA, fliE, fliF, iraP, nlpA, pepD, ubiT, wrbA, yccT | ||||||
Simple and complex regulons | BasR,BolA,BtsR,CRP,CpxR,Cra,CsgD,FliZ,H-NS,IHF,MlrA,MqsA,OmpR,RcdA,RcsAB,RstA,ppGpp BasR,BtsR,CRP,CpxR,Cra,CsgD,FliZ,H-NS,IHF,MlrA,MqsA,OmpR,RcdA,RcsAB,RstA BtsR,CpxR,CsgD,FliZ CsgD CsgD,DksA-ppGpp,ppGpp Read more > | ||||||
Simple and complex regulatory phrases | Regulatory phrase (List of promoters regulated by the phrase) |
Transcription factor regulation |
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Functional conformation | Function | Promoter | Sigma factor | Central Rel-Pos | Distance to first Gene | Genes | Sequence![]() |
LeftPos | RightPos | Evidence (Confirmed, Strong, Weak) | References | |
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CsgD | activator | adrAp | Sigma38 | -65.5 | -81.5 | dgcC |
ctgatagtgcTAACGGGTGAGCTACgaaaatggct
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403615 | 403629 | [GEA], [AIBSCS], [APIORCISFBSCS], [BPP], [SM] | [1], [2] | |
CsgD | activator | adrAp | Sigma38 | -47.0 | -63.0 | dgcC |
gctacgaaaaTGGCTCACCCGaaatatcata
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403635 | 403645 | [GEA], [AIBSCS], [SM] | [1] | |
CsgD | activator | csgBp | Sigma70 | -80.5 | -172.5 | csgB, csgA, csgC |
atttacgtggGTTTTAATACTTTGGtatgaactaa
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1103772 | 1103786 | [GEA], [APIORCISFBSCS], [BPP] | [2] | |
CsgD | activator | csgBp | Sigma70 | -57.5 | -149.5 | csgB, csgA, csgC |
ggtatgaactAAAAAAGAAAAATACaacgcgcggg
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1103795 | 1103809 | [GEA], [APIORCISFBSCS], [BPP] | [2] | |
CsgD | activator | csgBp | Sigma70 | -38.0 | -130.0 | csgB, csgA, csgC |
atacaacgcgCGGGTGAGTTAttaaaaatat
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1103816 | 1103826 | [GEA], [AIBSCS], [SM] | [1] | |
CsgD | activator | csgBp | Sigma70 | -27.5 | -119.5 | csgB, csgA, csgC |
gcgggtgagtTATTAAAAATATTTCcgcagacata
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1103825 | 1103839 | [GEA], [APIORCISFBSCS], [BPP] | [2] | |
CsgD | activator | csgBp2 | Sigma38 | -80.5 | -172.5 | csgB, csgA, csgC |
atttacgtggGTTTTAATACTTTGGtatgaactaa
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1103772 | 1103786 | [GEA], [APIORCISFBSCS], [BPP] | [2] | |
CsgD | activator | csgBp2 | Sigma38 | -57.5 | -149.5 | csgB, csgA, csgC |
ggtatgaactAAAAAAGAAAAATACaacgcgcggg
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1103795 | 1103809 | [GEA], [APIORCISFBSCS], [BPP] | [2] | |
CsgD | activator | csgBp2 | Sigma38 | -38.0 | -130.0 | csgB, csgA, csgC |
atacaacgcgCGGGTGAGTTAttaaaaatat
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1103816 | 1103826 | [GEA], [AIBSCS], [SM] | [1] | |
CsgD | activator | csgBp2 | Sigma38 | -27.5 | -119.5 | csgB, csgA, csgC |
gcgggtgagtTATTAAAAATATTTCcgcagacata
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1103825 | 1103839 | [GEA], [APIORCISFBSCS], [BPP] | [2] | |
CsgD | activator | csgDp1 | Sigma70 | -166.5 | -314.5 | csgD, csgE, csgF, csgG |
gcattattagTAAGTTATCACCATTtgtatgattt
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1103504 | 1103518 | [GEA], [APIORCISFBSCS], [BPP] | [2] | |
CsgD | activator | csgDp1 | Sigma70 | -118.5 | -266.5 | csgD, csgE, csgF, csgG |
aataaaaaccAAATGTACAACTTTTctatcatttc
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1103456 | 1103470 | [GEA], [APIORCISFBSCS], [BPP] | [2] | |
CsgD | activator | csgDp1 | Sigma70 | 9.5 | -139.5 | csgD, csgE, csgF, csgG |
gattgaaatcAGATGTAATCCATTAgttttatatt
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1103329 | 1103343 | [GEA], [APIORCISFBSCS], [BPP] | [2] | |
CsgD | activator | csgDp1 | Sigma70 | 29.5 | -119.5 | csgD, csgE, csgF, csgG |
cattagttttATATTTTACCCATTTagggctgatt
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1103309 | 1103323 | [GEA], [APIORCISFBSCS], [BPP] | [2] | |
CsgD | activator | csgDp3 | Sigma38 | -166.5 | -314.5 | csgD, csgE, csgF, csgG |
gcattattagTAAGTTATCACCATTtgtatgattt
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1103504 | 1103518 | [GEA], [APIORCISFBSCS], [BPP] | [2] | |
CsgD | activator | csgDp3 | Sigma38 | -118.5 | -266.5 | csgD, csgE, csgF, csgG |
aataaaaaccAAATGTACAACTTTTctatcatttc
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1103456 | 1103470 | [GEA], [APIORCISFBSCS], [BPP] | [2] | |
CsgD | activator | csgDp3 | Sigma38 | 9.5 | -139.5 | csgD, csgE, csgF, csgG |
gattgaaatcAGATGTAATCCATTAgttttatatt
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1103329 | 1103343 | [GEA], [APIORCISFBSCS], [BPP] | [2] | |
CsgD | activator | csgDp3 | Sigma38 | 29.5 | -119.5 | csgD, csgE, csgF, csgG |
cattagttttATATTTTACCCATTTagggctgatt
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1103309 | 1103323 | [GEA], [APIORCISFBSCS], [BPP] | [2] | |
CsgD | repressor | flgMp | Sigma28 | 1.5 | -36.5 | flgM, flgN |
cttgccgataAATAAGCAACACATGataaaagcgc
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1130158 | 1130172 | [APIORCISFBSCS], [BPP] | [3] | |
CsgD | repressor | flgMp | Sigma28 | 17.5 | -20.5 | flgM, flgN |
caacacatgaTAAAAGCGCCCTCAAtgaggaataa
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1130142 | 1130156 | [APIORCISFBSCS], [BPP] | [3] | |
CsgD | repressor | fliAp1 | Sigma70 | -10.5 | -40.5 | fliA, fliZ, tcyJ |
aaaccctgcaGAAACGGATAATCATgccgataact
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2001823 | 2001837 | [AIBSCS], [BPP] | [3] | |
CsgD | repressor | fliEp1 | Sigma70 | -39.5 | -61.5 | fliE |
ttttttgttgCTATTTAGCGCCTTTgtcttattga
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2013069 | 2013083 | [APIORCISFBSCS], [BPP], [GEA], [APIORCISFBSCS], [BPP] | [2] | |
CsgD | repressor | fliEp1 | Sigma70 | -24.5 | -46.5 | fliE |
tagcgcctttGTCTTATTGACTTACtggtaggctt
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2013054 | 2013068 | [APIORCISFBSCS], [BPP], [GEA], [APIORCISFBSCS], [BPP] | [2] | |
CsgD | repressor | fliEp2 | Sigma28 | 18.5 | -61.5 | fliE |
ttttttgttgCTATTTAGCGCCTTTgtcttattga
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2013069 | 2013083 | [APIORCISFBSCS], [BPP], [GEA], [APIORCISFBSCS], [BPP] | [2] | |
CsgD | repressor | fliEp2 | Sigma28 | 33.5 | -46.5 | fliE |
tagcgcctttGTCTTATTGACTTACtggtaggctt
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2013054 | 2013068 | [APIORCISFBSCS], [BPP], [GEA], [APIORCISFBSCS], [BPP] | [2] | |
CsgD | repressor | fliFp1 | Sigma70 | -85.5 | -168.5 | fliF, fliG, fliH, fliI, fliJ, fliK |
aagcctaccaGTAAGTCAATAAGACaaaggcgcta
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2013054 | 2013068 | [GEA], [APIORCISFBSCS], [BPP] | [2] | |
CsgD | repressor | fliFp1 | Sigma70 | -70.5 | -153.5 | fliF, fliG, fliH, fliI, fliJ, fliK |
tcaataagacAAAGGCGCTAAATAGcaacaaaaaa
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2013069 | 2013083 | [GEA], [APIORCISFBSCS], [BPP] | [2] | |
CsgD | activator | iraPp1 | Sigma70 | nd | nd | iraP | nd | nd | [GEA], [BPP] | [4], [5] | ||
CsgD | activator | nlpAp | nd | -91.5 | -115.5 | nlpA |
cgtggtcagtAAGAAGTGCCAGACTttatattcca
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3840102 | 3840116 | [GEA], [BPP] | [2] | |
CsgD | activator | nlpAp | nd | -76.5 | -100.5 | nlpA |
gtgccagactTTATATTCCACTTTTattccttttt
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3840087 | 3840101 | [GEA], [APIORCISFBSCS], [BPP] | [2] | |
CsgD | repressor | pepDp3 | Sigma70 | 2.0 | -20.0 | pepD |
tactgttttgCGGGTGATCGAcaaggagact
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255731 | 255741 | [GEA], [AIBSCS] | [1] | |
CsgD | repressor | ubiTp2 | nd | -12.5 | -37.5 | ubiT, yhbS |
gttatttttcTGATATGGCAAAATAggatgattgt
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3301307 | 3301321 | [GEA], [APIORCISFBSCS], [BPP] | [2] | |
CsgD | repressor | ubiTp2 | nd | 15.5 | -10.5 | ubiT, yhbS |
atgattgttgAAACAGGGAGTAAAActcgtgttgg
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3301280 | 3301294 | [GEA], [APIORCISFBSCS], [BPP] | [2] | |
CsgD | activator | wrbAp | Sigma38 | -166.5 | -216.5 | wrbA, yccJ |
gcttcttagcGAGAATAGATATCATctccaataat
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1067918 | 1067932 | [APIORCISFBSCS], [BPP] | [2] | |
CsgD | activator | wrbAp | Sigma38 | -136.5 | -186.5 | wrbA, yccJ |
ataattatccATAAGCCGCTCTTATgattaaaaaa
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1067888 | 1067902 | [APIORCISFBSCS], [BPP] | [2] | |
CsgD | activator | wrbAp | Sigma38 | -114.5 | -164.5 | wrbA, yccJ |
tatgattaaaAAAACGCGATGAGATaaaaatgtgt
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1067866 | 1067880 | [APIORCISFBSCS], [BPP] | [2] | |
CsgD | activator | yccTp | nd | -42.5 | -106.5 | yccT |
aaccatgcagCTAATACGAATGAATgagagcaaaa
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1027873 | 1027887 | [GEA], [APIORCISFBSCS], [BPP] | [2] |
Alignment and PSSM for CsgD TFBSs | ![]() |
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Aligned TFBS of CsgD |
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Sequence | |
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AAAATGGCTCACCC | |
TAAATGGGTAAAAT | |
TAAGTCAATAAGAC | |
CTAATGGATTACAT | |
AAAGGCGCTAAATA | |
TAAATAAGCAACAC | |
TTAATAACTCACCC | |
AGAATAGATATCAT | |
CAAATGGTGATAAC | |
CTTGTCGATCACCC | |
ACAGGGAGTAAAAC | |
AAAAGCGCCCTCAA | |
GAAACGGATAATCA | |
CAAAGTATTAAAAC | |
AAAGTGGAATATAA | |
CAAATGTACAACTT | |
TTCGTAGCTCACCC | |
TAAGCCGCTCTTAT | |
CGATGAGATAAAAA | |
TGAGTTATTAAAAA | |
AAAAAGAAAAATAC | |
GATATGGCAAAATA | |
AAAGTCTGGCACTT | |
CGAATGAATGAGAG |
Position weight matrix (PWM). CsgD matrix-quality result |
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A 8 15 21 14 1 5 8 10 3 14 20 8 15 7 C 7 1 1 0 2 6 0 7 3 7 0 10 5 10 G 2 4 0 9 5 11 14 4 2 1 0 2 0 1 T 7 4 2 1 16 2 2 3 16 2 4 4 4 6 |
Consensus |
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; consensus.strict caAatgGataAcac ; consensus.strict.rc GTGTTATCCATTTG ; consensus.IUPAC maArksRmtmAmmm ; consensus.IUPAC.rc KKKTKAKYSMYTTK ; consensus.regexp [ac]aA[ag][gt][cg][AG][ac]t[ac]A[ac][ac][ac] ; consensus.regexp.rc [GT][GT][GT]T[GT]A[GT][CT][CG][AC][CT]TT[GT] |
Evolutionary conservation of regulatory elements | ![]() |
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Reference(s) |
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