NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|488982216|ref|WP_002893035|]
View 

MULTISPECIES: RamA family antibiotic efflux transcriptional regulator [Bacteria]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
ramA_TF NF012144
RamA family antibiotic efflux transcriptional regulator;
2-109 1.27e-81

RamA family antibiotic efflux transcriptional regulator;


:

Pssm-ID: 411085 [Multi-domain]  Cd Length: 108  Bit Score: 233.83  E-value: 1.27e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488982216   2 TISAQVIDTIVEWIDDNLHQPLRIDDIARHAGYSKWHLQRLFLQYKGESLGRYIRERKLLLAARDLRDTDQRVYDICLKY 81
Cdd:NF012144   1 TISAQVIDTIVEWIDDNLHQPLRIDDIARHAGYSKWHLQRLFLQYKGESLGRYIRERKLLLAARDLRDTDQKVYDICLKY 80

                         90       100
                 ....*....|....*....|....*...
gi 488982216  82 GFDSQQTFTRVFTRTFNQPPGAYRKENH 109
Cdd:NF012144  81 GFDSQQTFTRIFTRTFNQPPGAYRKENH 108
 
Name Accession Description Interval E-value
ramA_TF NF012144
RamA family antibiotic efflux transcriptional regulator;
2-109 1.27e-81

RamA family antibiotic efflux transcriptional regulator;


Pssm-ID: 411085 [Multi-domain]  Cd Length: 108  Bit Score: 233.83  E-value: 1.27e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488982216   2 TISAQVIDTIVEWIDDNLHQPLRIDDIARHAGYSKWHLQRLFLQYKGESLGRYIRERKLLLAARDLRDTDQRVYDICLKY 81
Cdd:NF012144   1 TISAQVIDTIVEWIDDNLHQPLRIDDIARHAGYSKWHLQRLFLQYKGESLGRYIRERKLLLAARDLRDTDQKVYDICLKY 80

                         90       100
                 ....*....|....*....|....*...
gi 488982216  82 GFDSQQTFTRVFTRTFNQPPGAYRKENH 109
Cdd:NF012144  81 GFDSQQTFTRIFTRTFNQPPGAYRKENH 108
PRK10219 PRK10219
superoxide response transcriptional regulator SoxS;
6-105 1.18e-39

superoxide response transcriptional regulator SoxS;


Pssm-ID: 182314 [Multi-domain]  Cd Length: 107  Bit Score: 127.73  E-value: 1.18e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488982216   6 QVIDTIVEWIDDNLHQPLRIDDIARHAGYSKWHLQRLFLQYKGESLGRYIRERKLLLAARDLRDTDQRVYDICLKYGFDS 85
Cdd:PRK10219   5 KIIQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELRTTERPIFDIAMDLGYVS 84

                         90       100
                 ....*....|....*....|
gi 488982216  86 QQTFTRVFTRTFNQPPGAYR 105
Cdd:PRK10219  85 QQTFSRVFRRQFDRTPSDYR 104
RobA_TF NF012228
MDR efflux pump AcrAB transcriptional activator RobA; The original characterization of RobA as ...
 5-106 1.31e-36

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: 125.40  E-value: 1.31e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488982216   5 AQVIDTIVEWIDDNLHQPLRIDDIARHAGYSKWHLQRLFLQYKGESLGRYIRERKLLLAARDLRDTDQRVYDICLKYGFD 84
Cdd:NF012228   2 AGIIRDLLVWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGQAIGAYIRARRLSKAAVALRLTSRPILDIALQYRFD 81

                         90       100
                 ....*....|....*....|..
gi 488982216  85 SQQTFTRVFTRTFNQPPGAYRK 106
Cdd:NF012228  82 SQQTFTRAFKKQFNQTPALYRR 103
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
22-105 5.12e-32

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 107.64  E-value: 5.12e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488982216    22 PLRIDDIARHAGYSKWHLQRLFLQYKGESLGRYIRERKLLLAARDLRDTDQRVYDICLKYGFDSQQTFTRVFTRTFNQPP 101
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 488982216   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 2.76e-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: 96.38  E-value: 2.76e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488982216   8 IDTIVEWIDDNLHQPLRIDDIARHAGYSKWHLQRLFLQYKGESLGRYIRERKLLLAARDLRDTDQRVYDICLKYGFDSQQ 87
Cdd:COG4977  212 LARAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLLETTDLSIEEIAAACGFGSAS 291

                         90       100
                 ....*....|....*....|....*
gi 488982216  88 TFTRVFTRTFNQPPGAYRKENHSRA 112
Cdd:COG4977  292 HFRRAFRRRFGVSPSAYRRRFRARA 316
HTH_18 pfam12833
Helix-turn-helix domain;
28-106 1.53e-22

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 83.41  E-value: 1.53e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488982216   28 IARHAGYSKWHLQRLFLQYKGESLGRYIRERKLLLAARDL-RDTDQRVYDICLKYGFDSQQTFTRVFTRTFNQPPGAYRK 106
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLlEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80
 
Name Accession Description Interval E-value
ramA_TF NF012144
RamA family antibiotic efflux transcriptional regulator;
2-109 1.27e-81

RamA family antibiotic efflux transcriptional regulator;


Pssm-ID: 411085 [Multi-domain]  Cd Length: 108  Bit Score: 233.83  E-value: 1.27e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488982216   2 TISAQVIDTIVEWIDDNLHQPLRIDDIARHAGYSKWHLQRLFLQYKGESLGRYIRERKLLLAARDLRDTDQRVYDICLKY 81
Cdd:NF012144   1 TISAQVIDTIVEWIDDNLHQPLRIDDIARHAGYSKWHLQRLFLQYKGESLGRYIRERKLLLAARDLRDTDQKVYDICLKY 80

                         90       100
                 ....*....|....*....|....*...
gi 488982216  82 GFDSQQTFTRVFTRTFNQPPGAYRKENH 109
Cdd:NF012144  81 GFDSQQTFTRIFTRTFNQPPGAYRKENH 108
PRK10219 PRK10219
superoxide response transcriptional regulator SoxS;
6-105 1.18e-39

superoxide response transcriptional regulator SoxS;


Pssm-ID: 182314 [Multi-domain]  Cd Length: 107  Bit Score: 127.73  E-value: 1.18e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488982216   6 QVIDTIVEWIDDNLHQPLRIDDIARHAGYSKWHLQRLFLQYKGESLGRYIRERKLLLAARDLRDTDQRVYDICLKYGFDS 85
Cdd:PRK10219   5 KIIQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLLAAVELRTTERPIFDIAMDLGYVS 84

                         90       100
                 ....*....|....*....|
gi 488982216  86 QQTFTRVFTRTFNQPPGAYR 105
Cdd:PRK10219  85 QQTFSRVFRRQFDRTPSDYR 104
RobA_TF NF012228
MDR efflux pump AcrAB transcriptional activator RobA; The original characterization of RobA as ...
 5-106 1.31e-36

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: 125.40  E-value: 1.31e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488982216   5 AQVIDTIVEWIDDNLHQPLRIDDIARHAGYSKWHLQRLFLQYKGESLGRYIRERKLLLAARDLRDTDQRVYDICLKYGFD 84
Cdd:NF012228   2 AGIIRDLLVWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGQAIGAYIRARRLSKAAVALRLTSRPILDIALQYRFD 81

                         90       100
                 ....*....|....*....|..
gi 488982216  85 SQQTFTRVFTRTFNQPPGAYRK 106
Cdd:NF012228  82 SQQTFTRAFKKQFNQTPALYRR 103
PRK15121 PRK15121
MDR efflux pump AcrAB transcriptional activator RobA;
5-107 1.83e-35

MDR efflux pump AcrAB transcriptional activator RobA;


Pssm-ID: 185076 [Multi-domain]  Cd Length: 289  Bit Score: 122.42  E-value: 1.83e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488982216   5 AQVIDTIVEWIDDNLHQPLRIDDIARHAGYSKWHLQRLFLQYKGESLGRYIRERKLLLAARDLRDTDQRVYDICLKYGFD 84
Cdd:PRK15121   4 AGIIRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGHAIGAYIRARRLSKAAVALRLTSRPILDIALQYRFD 83

                         90       100
                 ....*....|....*....|...
gi 488982216  85 SQQTFTRVFTRTFNQPPGAYRKE 107
Cdd:PRK15121  84 SQQTFTRAFKKQFAQTPALYRRS 106
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
22-105 5.12e-32

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 107.64  E-value: 5.12e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488982216    22 PLRIDDIARHAGYSKWHLQRLFLQYKGESLGRYIRERKLLLAARDLRDTDQRVYDICLKYGFDSQQTFTRVFTRTFNQPP 101
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 488982216   102 GAYR 105
Cdd:smart00342  81 SEYR 84
PRK11511 PRK11511
MDR efflux pump AcrAB transcriptional activator MarA;
5-108 5.69e-32

MDR efflux pump AcrAB transcriptional activator MarA;


Pssm-ID: 236920 [Multi-domain]  Cd Length: 127  Bit Score: 109.04  E-value: 5.69e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488982216   5 AQVIDTIVEWIDDNLHQPLRIDDIARHAGYSKWHLQRLFLQYKGESLGRYIRERKLLLAARDLRDTDQRVYDICLKYGFD 84
Cdd:PRK11511   8 AITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKLKESNEPILYLAERYGFE 87

                         90       100
                 ....*....|....*....|....
gi 488982216  85 SQQTFTRVFTRTFNQPPGAYRKEN 108
Cdd:PRK11511  88 SQQTLTRTFKNYFDVPPHKYRMTN 111
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 8-112 2.76e-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: 96.38  E-value: 2.76e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488982216   8 IDTIVEWIDDNLHQPLRIDDIARHAGYSKWHLQRLFLQYKGESLGRYIRERKLLLAARDLRDTDQRVYDICLKYGFDSQQ 87
Cdd:COG4977  212 LARAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLLETTDLSIEEIAAACGFGSAS 291

                         90       100
                 ....*....|....*....|....*
gi 488982216  88 TFTRVFTRTFNQPPGAYRKENHSRA 112
Cdd:COG4977  292 HFRRAFRRRFGVSPSAYRRRFRARA 316
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
19-112 2.96e-24

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 92.92  E-value: 2.96e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488982216  19 LHQPLRIDDIARHAGYSKWHLQRLFLQYKGESLGRYIRERKLLLAARDLRDTDQRVYDICLKYGFDSQQTFTRVFTRTFN 98
Cdd:COG2207  165 LLLLLTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFG 244

                         90
                 ....*....|....
gi 488982216  99 QPPGAYRKENHSRA 112
Cdd:COG2207  245 VTPSEYRKRLRARA 258
HTH_18 pfam12833
Helix-turn-helix domain;
28-106 1.53e-22

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 83.41  E-value: 1.53e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488982216   28 IARHAGYSKWHLQRLFLQYKGESLGRYIRERKLLLAARDL-RDTDQRVYDICLKYGFDSQQTFTRVFTRTFNQPPGAYRK 106
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLlEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 5-106 2.67e-16

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: 72.78  E-value: 2.67e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488982216   5 AQVIDTIVEWIDDNLHQPLRIDDIARHAGYSKWHLQRLFLQYKGESLGRYIRERKLLLaARDLRDTDQRVYDICLKYGFD 84
Cdd:COG2169   83 ADLVARACRLIEAGAEDRPSLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLR-ARQLLQTGLSVTDAAYAAGFG 161

                         90       100
                 ....*....|....*....|..
gi 488982216  85 SQQTFTRVFTRTFNQPPGAYRK 106
Cdd:COG2169  162 SLSRFYEAFKKLLGMTPSAYRR 183
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 15-106 1.78e-14

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 67.36  E-value: 1.78e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488982216  15 IDDNLHQP-LRIDDIARHAGYSKWHLQRLFLQyKGESLGRYIRERKLLLAARDLRD--TDQRVYDICLKYGFDSQQTFTR 91
Cdd:PRK09685 206 IDQSIQEEiLRPEWIAGELGISVRSLYRLFAE-QGLVVAQYIRNRRLDRCADDLRPaaDDEKITSIAYKWGFSDSSHFST 284

                         90
                 ....*....|....*
gi 488982216  92 VFTRTFNQPPGAYRK 106
Cdd:PRK09685 285 AFKQRFGVSPGEYRR 299
PRK10371 PRK10371
transcriptional regulator MelR;
8-113 8.93e-12

transcriptional regulator MelR;


Pssm-ID: 182416 [Multi-domain]  Cd Length: 302  Bit Score: 59.83  E-value: 8.93e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488982216   8 IDTIVEWIDDNLHQPLRIDDIARHAGYSKWHLQRLFLQYKGESLGRYIRERKLLLAARDLRDTDQRVYDICLKYGFDSQQ 87
Cdd:PRK10371 193 VSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRALLSDTDKSILDIALTAGFRSSS 272

                         90       100
                 ....*....|....*....|....*.
gi 488982216  88 TFTRVFTRTFNQPPGAYRKENHSRAH 113
Cdd:PRK10371 273 RFYSTFGKYVGMSPQQYRKLSQQRRQ 298
ftrA PRK09393
transcriptional activator FtrA; Provisional
 11-106 1.06e-11

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 59.59  E-value: 1.06e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488982216  11 IVEWIDDNLHQPLRIDDIARHAGYSKWHLQRLFLQYKGESLGRY-IRERklLLAARDLRDTDQ-RVYDICLKYGFDSQQT 88
Cdd:PRK09393 223 LIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPAEWlLRER--LARARDLLESSAlSIDQIAERAGFGSEES 300

                         90
                 ....*....|....*...
gi 488982216  89 FTRVFTRTFNQPPGAYRK 106
Cdd:PRK09393 301 LRHHFRRRAATSPAAYRK 318
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
8-107 1.72e-09

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 53.37  E-value: 1.72e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488982216   8 IDTIVEWIDDNLHQPLRIDDIARHAGYSKWHLQRLFLQYKGESLGRYIRERKLLLAARDLRDTDQRVYDICLKYGFDSQQ 87
Cdd:PRK13501 178 LDLIMSALQQSLGAYFDMADFCHKNQLVERSLKQLFRQQTGMSISHYLRQIRLCHAKCLLRGSEHRISDIAARCGFEDSN 257

                         90       100
                 ....*....|....*....|
gi 488982216  88 TFTRVFTRTFNQPPGAYRKE 107
Cdd:PRK13501 258 YFSAVFTREAGMTPRDYRQR 277
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
8-106 3.00e-08

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 49.59  E-value: 3.00e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488982216   8 IDTIVEWIDDNLHQPLRIDDIARHAGYSKWHLQRLFLQYKGESLGRYIRERKLLLAARDLRDTDQRVYDICLKYGFDSQQ 87
Cdd:PRK10572 185 VREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRAKLLLQTTRMPIATIGRNVGYDDQL 264

                         90
                 ....*....|....*....
gi 488982216  88 TFTRVFTRTFNQPPGAYRK 106
Cdd:PRK10572 265 YFSRVFKKCTGASPSEFRA 283
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 15-56 2.03e-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: 2.03e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 488982216   15 IDDNLHQPLRIDDIARHAGYSKWHLQRLFLQYKGESLGRYIR 56
Cdd:pfam00165   1 LRENLSTNLTIADIADELGFSRSYFSRLFKKYTGVTPSQYRH 42
PRK13500 PRK13500
HTH-type transcriptional activator RhaR;
2-111 4.99e-07

HTH-type transcriptional activator RhaR;


Pssm-ID: 184091 [Multi-domain]  Cd Length: 312  Bit Score: 46.25  E-value: 4.99e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488982216   2 TISAQVIDTIVEWIDDNLHQPLRIDDIARHAGYSKWHLQRLFLQYKGESLGRYIRERKLLLAARDLRDTDQRVYDICLKY 81
Cdd:PRK13500 202 TSSETLLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHSRLLISDISTEC 281

                         90       100       110
                 ....*....|....*....|....*....|
gi 488982216  82 GFDSQQTFTRVFTRTFNQPPGAYRKENHSR 111
Cdd:PRK13500 282 GFEDSNYFSVVFTRETGMTPSQWRHLNSQK 311
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
7-105 4.34e-05

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 40.81  E-value: 4.34e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488982216   7 VIDTIVEWIDDNLHQPLRIDDIARHAGYSKWHLQRLFLQYKGESLGRYIRERKLLLAARDLRDTDQRVYDICLKYGFDSQ 86
Cdd:PRK13502 177 LLDKLITALANSLECPFALDAFCQQEQCSERVLRQQFRAQTGMTINQYLRQVRICHAQYLLQHSPLMISEISMQCGFEDS 256

                         90
                 ....*....|....*....
gi 488982216  87 QTFTRVFTRTFNQPPGAYR 105
Cdd:PRK13502 257 NYFSVVFTRETGMTPSQWR 275
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
14-105 1.08e-04

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 39.66  E-value: 1.08e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488982216  14 WIDDNLHQPLRIDDIARHAGYSKWHLQRLFLQYKGESLGRYIRERKLLLAARDLRDTDQRVYDICLKYGFDSQQTFTRVF 93
Cdd:PRK13503 179 WLEDHFAEEVNWEALADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDASVTDIAYRCGFGDSNHFSTLF 258

                         90
                 ....*....|..
gi 488982216  94 TRTFNQPPGAYR 105
Cdd:PRK13503 259 RREFSWSPRDIR 270
PRK10296 PRK10296
DNA-binding transcriptional regulator ChbR; Provisional
 6-106 2.40e-03

DNA-binding transcriptional regulator ChbR; Provisional


Pssm-ID: 182362 [Multi-domain]  Cd Length: 278  Bit Score: 35.89  E-value: 2.40e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488982216   6 QVIDTIVEWID---DNLHQPLRIDDIA-----RHAGYSKWHLQRLFLQYKGESLGRYIRERKLLLAARDLRDTDQRVYDI 77
Cdd:PRK10296 164 QVIDDIPQWLKatvEKMHDKEQFSESAlenmvRLSGKSQEYLTRATRRYYGKTPMQIINEIRINFAKKQLEMTNYSVTDI 243

                         90       100
                 ....*....|....*....|....*....
gi 488982216  78 CLKYGFDSQQTFTRVFTRTFNQPPGAYRK 106
Cdd:PRK10296 244 AFEAGYSSPSLFIKTFKKLTSFTPGSYRK 272
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 65-106 3.37e-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: 32.90  E-value: 3.37e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 488982216   65 RDLRDTDQRVYDICLKYGFdSQQTFTRVFTRTFNQPPGAYRK 106
Cdd:pfam00165   2 RENLSTNLTIADIADELGF-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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH