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Conserved domains on  [gi|489955573|ref|WP_003858880|]
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MULTISPECIES: RamA family antibiotic efflux transcriptional regulator [Enterobacter]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ramA_TF NF012144
RamA family antibiotic efflux transcriptional regulator;
2-109 9.90e-81

RamA family antibiotic efflux transcriptional regulator;


:

Pssm-ID: 411085 [Multi-domain]  Cd Length: 108  Bit Score: 231.52  E-value: 9.90e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489955573   2 TISAQVIDTIVEWIDDNLHQPLRIEEIARHAGYSKWHLQRLFMQYKGESLGRYIRERKLLMAARDLRESDERVYDICLRY 81
Cdd:NF012144   1 TISAQVIDTIVEWIDDNLHQPLRIDDIARHAGYSKWHLQRLFLQYKGESLGRYIRERKLLLAARDLRDTDQKVYDICLKY 80

                         90       100
                 ....*....|....*....|....*...
gi 489955573  82 GFDSQQTFTRIFTRTFNQPPGAYRKENH 109
Cdd:NF012144  81 GFDSQQTFTRIFTRTFNQPPGAYRKENH 108
 
Name Accession Description Interval E-value
ramA_TF NF012144
RamA family antibiotic efflux transcriptional regulator;
2-109 9.90e-81

RamA family antibiotic efflux transcriptional regulator;


Pssm-ID: 411085 [Multi-domain]  Cd Length: 108  Bit Score: 231.52  E-value: 9.90e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489955573   2 TISAQVIDTIVEWIDDNLHQPLRIEEIARHAGYSKWHLQRLFMQYKGESLGRYIRERKLLMAARDLRESDERVYDICLRY 81
Cdd:NF012144   1 TISAQVIDTIVEWIDDNLHQPLRIDDIARHAGYSKWHLQRLFLQYKGESLGRYIRERKLLLAARDLRDTDQKVYDICLKY 80

                         90       100
                 ....*....|....*....|....*...
gi 489955573  82 GFDSQQTFTRIFTRTFNQPPGAYRKENH 109
Cdd:NF012144  81 GFDSQQTFTRIFTRTFNQPPGAYRKENH 108
PRK10219 PRK10219
superoxide response transcriptional regulator SoxS;
6-105 7.43e-39

superoxide response transcriptional regulator SoxS;


Pssm-ID: 182314 [Multi-domain]  Cd Length: 107  Bit Score: 125.81  E-value: 7.43e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489955573   6 QVIDTIVEWIDDNLHQPLRIEEIARHAGYSKWHLQRLFMQYKGESLGRYIRERKLLMAARDLRESDERVYDICLRYGFDS 85
Cdd:PRK10219   5 KIIQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELRTTERPIFDIAMDLGYVS 84

                         90       100
                 ....*....|....*....|
gi 489955573  86 QQTFTRIFTRTFNQPPGAYR 105
Cdd:PRK10219  85 QQTFSRVFRRQFDRTPSDYR 104
RobA_TF NF012228
MDR efflux pump AcrAB transcriptional activator RobA; The original characterization of RobA as ...
 5-106 2.37e-34

MDR efflux pump AcrAB transcriptional activator RobA; The original characterization of RobA as a Right side Origin of replication Binding protein A (robA) may be misleading. Characterizations in large numbers of papers since then treat RobA as a transcriptional activator of the AcrAB antibiotic efflux pump.


Pssm-ID: 467958 [Multi-domain]  Cd Length: 286  Bit Score: 119.62  E-value: 2.37e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489955573   5 AQVIDTIVEWIDDNLHQPLRIEEIARHAGYSKWHLQRLFMQYKGESLGRYIRERKLLMAARDLRESDERVYDICLRYGFD 84
Cdd:NF012228   2 AGIIRDLLVWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGQAIGAYIRARRLSKAAVALRLTSRPILDIALQYRFD 81

                         90       100
                 ....*....|....*....|..
gi 489955573  85 SQQTFTRIFTRTFNQPPGAYRK 106
Cdd:NF012228  82 SQQTFTRAFKKQFNQTPALYRR 103
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
22-105 1.28e-30

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 104.17  E-value: 1.28e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489955573    22 PLRIEEIARHAGYSKWHLQRLFMQYKGESLGRYIRERKLLMAARDLRESDERVYDICLRYGFDSQQTFTRIFTRTFNQPP 101
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 489955573   102 GAYR 105
Cdd:smart00342  81 SEYR 84
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 8-112 6.38e-25

Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH domain [Transcription];


Pssm-ID: 444002 [Multi-domain]  Cd Length: 318  Bit Score: 95.61  E-value: 6.38e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489955573   8 IDTIVEWIDDNLHQPLRIEEIARHAGYSKWHLQRLFMQYKGESLGRYIRERKLLMAARDLRESDERVYDICLRYGFDSQQ 87
Cdd:COG4977  212 LARAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLLETTDLSIEEIAAACGFGSAS 291

                         90       100
                 ....*....|....*....|....*
gi 489955573  88 TFTRIFTRTFNQPPGAYRKENHGRA 112
Cdd:COG4977  292 HFRRAFRRRFGVSPSAYRRRFRARA 316
HTH_18 pfam12833
Helix-turn-helix domain;
28-106 3.04e-21

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 80.33  E-value: 3.04e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489955573   28 IARHAGYSKWHLQRLFMQYKGESLGRYIRERKLLMAARDL-RESDERVYDICLRYGFDSQQTFTRIFTRTFNQPPGAYRK 106
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLlEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80
 
Name Accession Description Interval E-value
ramA_TF NF012144
RamA family antibiotic efflux transcriptional regulator;
2-109 9.90e-81

RamA family antibiotic efflux transcriptional regulator;


Pssm-ID: 411085 [Multi-domain]  Cd Length: 108  Bit Score: 231.52  E-value: 9.90e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489955573   2 TISAQVIDTIVEWIDDNLHQPLRIEEIARHAGYSKWHLQRLFMQYKGESLGRYIRERKLLMAARDLRESDERVYDICLRY 81
Cdd:NF012144   1 TISAQVIDTIVEWIDDNLHQPLRIDDIARHAGYSKWHLQRLFLQYKGESLGRYIRERKLLLAARDLRDTDQKVYDICLKY 80

                         90       100
                 ....*....|....*....|....*...
gi 489955573  82 GFDSQQTFTRIFTRTFNQPPGAYRKENH 109
Cdd:NF012144  81 GFDSQQTFTRIFTRTFNQPPGAYRKENH 108
PRK10219 PRK10219
superoxide response transcriptional regulator SoxS;
6-105 7.43e-39

superoxide response transcriptional regulator SoxS;


Pssm-ID: 182314 [Multi-domain]  Cd Length: 107  Bit Score: 125.81  E-value: 7.43e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489955573   6 QVIDTIVEWIDDNLHQPLRIEEIARHAGYSKWHLQRLFMQYKGESLGRYIRERKLLMAARDLRESDERVYDICLRYGFDS 85
Cdd:PRK10219   5 KIIQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELRTTERPIFDIAMDLGYVS 84

                         90       100
                 ....*....|....*....|
gi 489955573  86 QQTFTRIFTRTFNQPPGAYR 105
Cdd:PRK10219  85 QQTFSRVFRRQFDRTPSDYR 104
PRK11511 PRK11511
MDR efflux pump AcrAB transcriptional activator MarA;
5-108 2.31e-34

MDR efflux pump AcrAB transcriptional activator MarA;


Pssm-ID: 236920 [Multi-domain]  Cd Length: 127  Bit Score: 115.20  E-value: 2.31e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489955573   5 AQVIDTIVEWIDDNLHQPLRIEEIARHAGYSKWHLQRLFMQYKGESLGRYIRERKLLMAARDLRESDERVYDICLRYGFD 84
Cdd:PRK11511   8 AITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYGFE 87

                         90       100
                 ....*....|....*....|....
gi 489955573  85 SQQTFTRIFTRTFNQPPGAYRKEN 108
Cdd:PRK11511  88 SQQTLTRTFKNYFDVPPHKYRMTN 111
RobA_TF NF012228
MDR efflux pump AcrAB transcriptional activator RobA; The original characterization of RobA as ...
 5-106 2.37e-34

MDR efflux pump AcrAB transcriptional activator RobA; The original characterization of RobA as a Right side Origin of replication Binding protein A (robA) may be misleading. Characterizations in large numbers of papers since then treat RobA as a transcriptional activator of the AcrAB antibiotic efflux pump.


Pssm-ID: 467958 [Multi-domain]  Cd Length: 286  Bit Score: 119.62  E-value: 2.37e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489955573   5 AQVIDTIVEWIDDNLHQPLRIEEIARHAGYSKWHLQRLFMQYKGESLGRYIRERKLLMAARDLRESDERVYDICLRYGFD 84
Cdd:NF012228   2 AGIIRDLLVWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGQAIGAYIRARRLSKAAVALRLTSRPILDIALQYRFD 81

                         90       100
                 ....*....|....*....|..
gi 489955573  85 SQQTFTRIFTRTFNQPPGAYRK 106
Cdd:NF012228  82 SQQTFTRAFKKQFNQTPALYRR 103
PRK15121 PRK15121
MDR efflux pump AcrAB transcriptional activator RobA;
5-107 1.72e-33

MDR efflux pump AcrAB transcriptional activator RobA;


Pssm-ID: 185076 [Multi-domain]  Cd Length: 289  Bit Score: 117.42  E-value: 1.72e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489955573   5 AQVIDTIVEWIDDNLHQPLRIEEIARHAGYSKWHLQRLFMQYKGESLGRYIRERKLLMAARDLRESDERVYDICLRYGFD 84
Cdd:PRK15121   4 AGIIRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGHAIGAYIRARRLSKAAVALRLTSRPILDIALQYRFD 83

                         90       100
                 ....*....|....*....|...
gi 489955573  85 SQQTFTRIFTRTFNQPPGAYRKE 107
Cdd:PRK15121  84 SQQTFTRAFKKQFAQTPALYRRS 106
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
22-105 1.28e-30

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 104.17  E-value: 1.28e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489955573    22 PLRIEEIARHAGYSKWHLQRLFMQYKGESLGRYIRERKLLMAARDLRESDERVYDICLRYGFDSQQTFTRIFTRTFNQPP 101
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 489955573   102 GAYR 105
Cdd:smart00342  81 SEYR 84
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 8-112 6.38e-25

Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH domain [Transcription];


Pssm-ID: 444002 [Multi-domain]  Cd Length: 318  Bit Score: 95.61  E-value: 6.38e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489955573   8 IDTIVEWIDDNLHQPLRIEEIARHAGYSKWHLQRLFMQYKGESLGRYIRERKLLMAARDLRESDERVYDICLRYGFDSQQ 87
Cdd:COG4977  212 LARAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLLETTDLSIEEIAAACGFGSAS 291

                         90       100
                 ....*....|....*....|....*
gi 489955573  88 TFTRIFTRTFNQPPGAYRKENHGRA 112
Cdd:COG4977  292 HFRRAFRRRFGVSPSAYRRRFRARA 316
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
19-112 7.63e-23

AraC-type DNA-binding domain and AraC-containing proteins [Transcription];


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 89.07  E-value: 7.63e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489955573  19 LHQPLRIEEIARHAGYSKWHLQRLFMQYKGESLGRYIRERKLLMAARDLRESDERVYDICLRYGFDSQQTFTRIFTRTFN 98
Cdd:COG2207  165 LLLLLTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFG 244

                         90
                 ....*....|....
gi 489955573  99 QPPGAYRKENHGRA 112
Cdd:COG2207  245 VTPSEYRKRLRARA 258
HTH_18 pfam12833
Helix-turn-helix domain;
28-106 3.04e-21

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 80.33  E-value: 3.04e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489955573   28 IARHAGYSKWHLQRLFMQYKGESLGRYIRERKLLMAARDL-RESDERVYDICLRYGFDSQQTFTRIFTRTFNQPPGAYRK 106
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLlEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 5-112 2.46e-15

Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), contains Zn-binding and two AraC-type DNA-binding domains [Replication, recombination and repair];


Pssm-ID: 441772 [Multi-domain]  Cd Length: 358  Bit Score: 70.08  E-value: 2.46e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489955573   5 AQVIDTIVEWIDDNLHQPLRIEEIARHAGYSKWHLQRLFMQYKGESLGRYIRERKLLmAARDLRESDERVYDICLRYGFD 84
Cdd:COG2169   83 ADLVARACRLIEAGAEDRPSLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLL-RARQLLQTGLSVTDAAYAAGFG 161

                         90       100
                 ....*....|....*....|....*...
gi 489955573  85 SQQTFTRIFTRTFNQPPGAYRKENHGRA 112
Cdd:COG2169  162 SLSRFYEAFKKLLGMTPSAYRRGGAGAA 189
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 15-106 2.81e-14

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 66.59  E-value: 2.81e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489955573  15 IDDNLHQP-LRIEEIARHAGYSKWHLQRLFMQyKGESLGRYIRERKLLMAARDLRE--SDERVYDICLRYGFDSQQTFTR 91
Cdd:PRK09685 206 IDQSIQEEiLRPEWIAGELGISVRSLYRLFAE-QGLVVAQYIRNRRLDRCADDLRPaaDDEKITSIAYKWGFSDSSHFST 284

                         90
                 ....*....|....*
gi 489955573  92 IFTRTFNQPPGAYRK 106
Cdd:PRK09685 285 AFKQRFGVSPGEYRR 299
ftrA PRK09393
transcriptional activator FtrA; Provisional
 11-106 5.67e-13

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 63.06  E-value: 5.67e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489955573  11 IVEWIDDNLHQPLRIEEIARHAGYSKWHLQRLFMQYKGESLGRY-IRERklLMAARDLRESD-ERVYDICLRYGFDSQQT 88
Cdd:PRK09393 223 LIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPAEWlLRER--LARARDLLESSaLSIDQIAERAGFGSEES 300

                         90
                 ....*....|....*...
gi 489955573  89 FTRIFTRTFNQPPGAYRK 106
Cdd:PRK09393 301 LRHHFRRRAATSPAAYRK 318
PRK10371 PRK10371
transcriptional regulator MelR;
8-113 5.29e-11

transcriptional regulator MelR;


Pssm-ID: 182416 [Multi-domain]  Cd Length: 302  Bit Score: 57.52  E-value: 5.29e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489955573   8 IDTIVEWIDDNLHQPLRIEEIARHAGYSKWHLQRLFMQYKGESLGRYIRERKLLMAARDLRESDERVYDICLRYGFDSQQ 87
Cdd:PRK10371 193 VSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRALLSDTDKSILDIALTAGFRSSS 272

                         90       100
                 ....*....|....*....|....*.
gi 489955573  88 TFTRIFTRTFNQPPGAYRKENHGRAH 113
Cdd:PRK10371 273 RFYSTFGKYVGMSPQQYRKLSQQRRQ 298
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
8-107 4.36e-10

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 54.91  E-value: 4.36e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489955573   8 IDTIVEWIDDNLHQPLRIEEIARHAGYSKWHLQRLFMQYKGESLGRYIRERKLLMAARDLRESDERVYDICLRYGFDSQQ 87
Cdd:PRK13501 178 LDLIMSALQQSLGAYFDMADFCHKNQLVERSLKQLFRQQTGMSISHYLRQIRLCHAKCLLRGSEHRISDIAARCGFEDSN 257

                         90       100
                 ....*....|....*....|
gi 489955573  88 TFTRIFTRTFNQPPGAYRKE 107
Cdd:PRK13501 258 YFSAVFTREAGMTPRDYRQR 277
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
8-106 1.60e-08

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 50.36  E-value: 1.60e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489955573   8 IDTIVEWIDDNLHQPLRIEEIARHAGYSKWHLQRLFMQYKGESLGRYiRERKLLMAARDL-RESDERVYDICLRYGFDSQ 86
Cdd:PRK10572 185 VREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRW-REDQRISRAKLLlQTTRMPIATIGRNVGYDDQ 263

                         90       100
                 ....*....|....*....|
gi 489955573  87 QTFTRIFTRTFNQPPGAYRK 106
Cdd:PRK10572 264 LYFSRVFKKCTGASPSEFRA 283
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
14-111 5.14e-08

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 48.90  E-value: 5.14e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489955573  14 WIDDNLHQPLRIEEIARHAGYSKWHLQRLFMQYKGESLGRYIRERKLLMAARDLRESDERVYDICLRYGFDSQQTFTRIF 93
Cdd:PRK13503 179 WLEDHFAEEVNWEALADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDASVTDIAYRCGFGDSNHFSTLF 258

                         90
                 ....*....|....*...
gi 489955573  94 TRTFNQPPgayRKENHGR 111
Cdd:PRK13503 259 RREFSWSP---RDIRQGR 273
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 15-56 2.10e-07

Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the N-terminal arm of AraC binds to the DNA binding domain (pfam00165) and helps to hold the two DNA binding domains in a relative orientation that favours DNA looping. In the presence of arabinose, the arms bind over the arabinose on the dimerization domain, thus freeing the DNA-binding domains. The freed DNA-binding domains are then able to assume a conformation suitable for binding to the adjacent DNA sites that are utilized when AraC activates transcription, and hence AraC ceases looping the DNA when arabinose is added.


Pssm-ID: 425497 [Multi-domain]  Cd Length: 42  Bit Score: 44.07  E-value: 2.10e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 489955573   15 IDDNLHQPLRIEEIARHAGYSKWHLQRLFMQYKGESLGRYIR 56
Cdd:pfam00165   1 LRENLSTNLTIADIADELGFSRSYFSRLFKKYTGVTPSQYRH 42
PRK13500 PRK13500
HTH-type transcriptional activator RhaR;
2-108 5.94e-07

HTH-type transcriptional activator RhaR;


Pssm-ID: 184091 [Multi-domain]  Cd Length: 312  Bit Score: 46.25  E-value: 5.94e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489955573   2 TISAQVIDTIVEWIDDNLHQPLRIEEIARHAGYSKWHLQRLFMQYKGESLGRYIRERKLLMAARDLRESDERVYDICLRY 81
Cdd:PRK13500 202 TSSETLLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHSRLLISDISTEC 281

                         90       100
                 ....*....|....*....|....*..
gi 489955573  82 GFDSQQTFTRIFTRTFNQPPGAYRKEN 108
Cdd:PRK13500 282 GFEDSNYFSVVFTRETGMTPSQWRHLN 308
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
7-105 1.25e-05

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 42.35  E-value: 1.25e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489955573   7 VIDTIVEWIDDNLHQPLRIEEIARHAGYSKWHLQRLFMQYKGESLGRYIRERKLLMAARDLRESDERVYDICLRYGFDSQ 86
Cdd:PRK13502 177 LLDKLITALANSLECPFALDAFCQQEQCSERVLRQQFRAQTGMTINQYLRQVRICHAQYLLQHSPLMISEISMQCGFEDS 256

                         90
                 ....*....|....*....
gi 489955573  87 QTFTRIFTRTFNQPPGAYR 105
Cdd:PRK13502 257 NYFSVVFTRETGMTPSQWR 275
PRK10296 PRK10296
DNA-binding transcriptional regulator ChbR; Provisional
 6-106 7.29e-03

DNA-binding transcriptional regulator ChbR; Provisional


Pssm-ID: 182362 [Multi-domain]  Cd Length: 278  Bit Score: 34.35  E-value: 7.29e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489955573   6 QVIDTIVEWID---DNLHQPLRIEEIA-----RHAGYSKWHLQRLFMQYKGESLGRYIRERKLLMAARDLRESDERVYDI 77
Cdd:PRK10296 164 QVIDDIPQWLKatvEKMHDKEQFSESAlenmvRLSGKSQEYLTRATRRYYGKTPMQIINEIRINFAKKQLEMTNYSVTDI 243

                         90       100
                 ....*....|....*....|....*....
gi 489955573  78 CLRYGFDSQQTFTRIFTRTFNQPPGAYRK 106
Cdd:PRK10296 244 AFEAGYSSPSLFIKTFKKLTSFTPGSYRK 272
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 70-106 8.36e-03

Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the N-terminal arm of AraC binds to the DNA binding domain (pfam00165) and helps to hold the two DNA binding domains in a relative orientation that favours DNA looping. In the presence of arabinose, the arms bind over the arabinose on the dimerization domain, thus freeing the DNA-binding domains. The freed DNA-binding domains are then able to assume a conformation suitable for binding to the adjacent DNA sites that are utilized when AraC activates transcription, and hence AraC ceases looping the DNA when arabinose is added.


Pssm-ID: 425497 [Multi-domain]  Cd Length: 42  Bit Score: 31.74  E-value: 8.36e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 489955573   70 SDERVYDICLRYGFdSQQTFTRIFTRTFNQPPGAYRK 106
Cdd:pfam00165   7 TNLTIADIADELGF-SRSYFSRLFKKYTGVTPSQYRH 42
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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