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Conserved domains on  [gi|1474091369|ref|WP_118505820|]
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MULTISPECIES: AraC family transcriptional regulator [Aquimarina]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 11454391)

helix-turn-helix (HTH) domain-containing protein with an AraC family HTH domain, binds DNA and may function as a transcriptional regulator

CATH:  1.10.10.60
Gene Ontology:  GO:0003700|GO:0003677
PubMed:  10473770|15808743|8831795

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
243-327 8.52e-18

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


:

Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 81.75  E-value: 8.52e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1474091369 243 SLKTLSIHFNTSESSMKRLLKS--NQTkFSNILEEILYNRAIHLLTKSDMNINLISENLGYSDSPNFIRSFKKWTGLTPG 320
Cdd:COG2207   170 TLEELARELGLSPRTLSRLFKEetGTS-PKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPS 248


                  ....*..
gi 1474091369 321 IYREHLR 327
Cdd:COG2207   249 EYRKRLR 255
 
Name Accession Description Interval E-value
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
243-327 8.52e-18

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 81.75  E-value: 8.52e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1474091369 243 SLKTLSIHFNTSESSMKRLLKS--NQTkFSNILEEILYNRAIHLLTKSDMNINLISENLGYSDSPNFIRSFKKWTGLTPG 320
Cdd:COG2207   170 TLEELARELGLSPRTLSRLFKEetGTS-PKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPS 248


                  ....*..
gi 1474091369 321 IYREHLR 327
Cdd:COG2207   249 EYRKRLR 255
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
242-323 2.95e-16

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 72.59  E-value: 2.95e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1474091369  242 PSLKTLSIHFNTSESSMKRLLKS-NQTKFSNILEEILYNRAIHLLTKSDMNINLISENLGYSDSPNFIRSFKKWTGLTPG 320
Cdd:smart00342   2 LTLEDLAEALGVSPRHLQRLFKKeTGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTPS 81


                   ...
gi 1474091369  321 IYR 323
Cdd:smart00342  82 EYR 84
HTH_18 pfam12833
Helix-turn-helix domain;
247-324 4.72e-13

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 63.76  E-value: 4.72e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1474091369 247 LSIHFNTSESSMKRLLKSN-QTKFSNILEEILYNRAIHLLTK-SDMNINLISENLGYSDSPNFIRSFKKWTGLTPGIYRE 324
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRElGLSPKEYLRRLRLERARRLLLEdTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
279-324 1.37e-06

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 49.20  E-value: 1.37e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1474091369 279 NRAIHLLTKSDMNINLISENLGYSDSPNFIRSFKKWTGLTPGIYRE 324
Cdd:PRK10572  238 SRAKLLLQTTRMPIATIGRNVGYDDQLYFSRVFKKCTGASPSEFRA 283
 
Name Accession Description Interval E-value
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
243-327 8.52e-18

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 81.75  E-value: 8.52e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1474091369 243 SLKTLSIHFNTSESSMKRLLKS--NQTkFSNILEEILYNRAIHLLTKSDMNINLISENLGYSDSPNFIRSFKKWTGLTPG 320
Cdd:COG2207   170 TLEELARELGLSPRTLSRLFKEetGTS-PKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPS 248


                  ....*..
gi 1474091369 321 IYREHLR 327
Cdd:COG2207   249 EYRKRLR 255
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
242-323 2.95e-16

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 72.59  E-value: 2.95e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1474091369  242 PSLKTLSIHFNTSESSMKRLLKS-NQTKFSNILEEILYNRAIHLLTKSDMNINLISENLGYSDSPNFIRSFKKWTGLTPG 320
Cdd:smart00342   2 LTLEDLAEALGVSPRHLQRLFKKeTGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTPS 81


                   ...
gi 1474091369  321 IYR 323
Cdd:smart00342  82 EYR 84
HTH_18 pfam12833
Helix-turn-helix domain;
247-324 4.72e-13

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 63.76  E-value: 4.72e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1474091369 247 LSIHFNTSESSMKRLLKSN-QTKFSNILEEILYNRAIHLLTK-SDMNINLISENLGYSDSPNFIRSFKKWTGLTPGIYRE 324
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRElGLSPKEYLRRLRLERARRLLLEdTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 280-329 1.26e-06

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: 49.39  E-value: 1.26e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1474091369 280 RAIHLLTKSDMNINLISENLGYSDSPNFIRSFKKWTGLTPGIYREHLRVS 329
Cdd:COG4977   266 RARRLLETTDLSIEEIAAACGFGSASHFRRAFRRRFGVSPSAYRRRFRAR 315
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
279-324 1.37e-06

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 49.20  E-value: 1.37e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1474091369 279 NRAIHLLTKSDMNINLISENLGYSDSPNFIRSFKKWTGLTPGIYRE 324
Cdd:PRK10572  238 SRAKLLLQTTRMPIATIGRNVGYDDQLYFSRVFKKCTGASPSEFRA 283
PRK15186 PRK15186
AraC family transcriptional regulator; Provisional
 190-329 1.94e-05

AraC family transcriptional regulator; Provisional


Pssm-ID: 185108 [Multi-domain]  Cd Length: 291  Bit Score: 45.44  E-value: 1.94e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1474091369 190 NRSEYKFVFSKSLLDTEVCAISLNSSIVPECQETNIINIIEQVISSYEcgcipSLKTLSIHFNTSESSMKRLLKSNQTKF 269
Cdd:PRK15186  151 DKKEYLIRFLLSEFIYEPEAFALFRELSQNTLAENIYNIIISDISRKW-----ALKDISDSLYMSCSTLKRKLKQENTSF 225

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1474091369 270 SNILEEILYNRAIHLLTKSDMNINLISENLGYSDSPNFIRSFKKWTGLTPGIYREHLRVS 329
Cdd:PRK15186  226 SEVYLNARMNKATKLLRNSEYNITRVAYMCGYDSASYFTCVFKKHFKTTPSEFLAFLSSS 285
PRK09978 PRK09978
DNA-binding transcriptional regulator GadX; Provisional
 254-324 5.21e-05

DNA-binding transcriptional regulator GadX; Provisional


Pssm-ID: 137624 [Multi-domain]  Cd Length: 274  Bit Score: 44.15  E-value: 5.21e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1474091369 254 SESSMKRLLKSNQTKFSNILEEILYNRAIHLLTKSDMNINLISENLGYSDSPNFIRSFKKWTGLTPGIYRE 324
Cdd:PRK09978  171 SPSLLKKKLREEETSYSQLLTECRMQRALQLIVIHGFSIKRVAVSCGYHSVSYFIYVFRNYYGMTPTEYQE 241
PRK15185 PRK15185
transcriptional regulator HilD; Provisional
 244-322 3.41e-04

transcriptional regulator HilD; Provisional


Pssm-ID: 185107 [Multi-domain]  Cd Length: 309  Bit Score: 41.90  E-value: 3.41e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1474091369 244 LKTLSIHFNTSESSMKRLLKSNQTKFSNILEEILYNRAIHLLTKSDMNINLISENLGYSDSPNFIRSFKKWTGLTPGIY 322
Cdd:PRK15185  225 LTDVADHIFMSTSTLKRKLAEEGTSFSDIYLSARMNQAAKLLRIGNHNVNAVALKCGYDSTSYFIQCFKKYFKTTPSTF 303
PRK10296 PRK10296
DNA-binding transcriptional regulator ChbR; Provisional
 272-326 3.82e-04

DNA-binding transcriptional regulator ChbR; Provisional


Pssm-ID: 182362 [Multi-domain]  Cd Length: 278  Bit Score: 41.67  E-value: 3.82e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1474091369 272 ILEEILYNRAIHLLTKSDMNINLISENLGYSDSPNFIRSFKKWTGLTPGIYREHL 326
Cdd:PRK10296  220 IINEIRINFAKKQLEMTNYSVTDIAFEAGYSSPSLFIKTFKKLTSFTPGSYRKKL 274
PRK09940 PRK09940
transcriptional regulator YdeO; Provisional
 254-319 4.06e-04

transcriptional regulator YdeO; Provisional


Pssm-ID: 182157 [Multi-domain]  Cd Length: 253  Bit Score: 41.22  E-value: 4.06e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1474091369 254 SESSMKRLLKSNQTKFSNILEEILYNRAIHLLtKSDMNINLISENLGYSDSPNFIRSFKKWTGLTP 319
Cdd:PRK09940  163 SESLLKKKLKQEQTTFSQILLDARMQHAKNLI-RVEGSVNKIAEQCGYASTSYFIYAFRKHFGNSP 227
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
254-324 1.98e-03

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 39.50  E-value: 1.98e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1474091369 254 SESSMKRLLKsNQTKFS--NILEEILYNRAIHLLTKSDMNINLISENLGYSDSPNFIRSFKKWTGLTPGIYRE 324
Cdd:PRK13501  205 VERSLKQLFR-QQTGMSisHYLRQIRLCHAKCLLRGSEHRISDIAARCGFEDSNYFSAVFTREAGMTPRDYRQ 276
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 282-323 3.07e-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: 34.82  E-value: 3.07e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1474091369 282 IHLLTKSDMNINLISENLGYSdSPNFIRSFKKWTGLTPGIYR 323
Cdd:pfam00165   1 LRENLSTNLTIADIADELGFS-RSYFSRLFKKYTGVTPSQYR 41
 
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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