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Conserved domains on  [gi|2163934930|ref|WP_231572277|]
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MULTISPECIES: helix-turn-helix domain-containing protein [Burkholderia]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 12122938)

helix-turn-helix (HTH) domain-containing protein binds DNA and may function as a transcriptional regulator

Gene Ontology:  GO:0003677
PubMed:  15808743

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_18 pfam12833
Helix-turn-helix domain;
74-149 1.09e-25

Helix-turn-helix domain;


:

Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 93.04  E-value: 1.09e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2163934930  74 WADEAGASTRTLARLFLAETGISFVHWRQLVRVQHALPLLA--SGMPVAEVSLALGYETPGAFAAMFRRVTGTTPSAY 149
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLedTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEY 78
 
Name Accession Description Interval E-value
HTH_18 pfam12833
Helix-turn-helix domain;
74-149 1.09e-25

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 93.04  E-value: 1.09e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2163934930  74 WADEAGASTRTLARLFLAETGISFVHWRQLVRVQHALPLLA--SGMPVAEVSLALGYETPGAFAAMFRRVTGTTPSAY 149
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLedTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEY 78
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
70-149 1.00e-23

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 88.38  E-value: 1.00e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2163934930   70 TLDAWADEAGASTRTLARLFLAETGISFVHWRQLVRVQHALPLLASG-MPVAEVSLALGYETPGAFAAMFRRVTGTTPSA 148
Cdd:smart00342   3 TLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTdLSVTEIALRVGFSSQSYFSRAFKKLFGVTPSE 82


                   .
gi 2163934930  149 Y 149
Cdd:smart00342  83 Y 83
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
60-149 8.26e-23

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 90.61  E-value: 8.26e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2163934930  60 AILRDPADVRTLDAWADEAGASTRTLARLFLAETGISFVHWRQLVRVQHALPLLASG-MPVAEVSLALGYETPGAFAAMF 138
Cdd:COG2207   160 LLLLLLLLLLTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETdLSISEIAYELGFSSQSHFSRAF 239

                          90
                  ....*....|.
gi 2163934930 139 RRVTGTTPSAY 149
Cdd:COG2207   240 KKRFGVTPSEY 250
ftrA PRK09393
transcriptional activator FtrA; Provisional
 46-149 7.53e-13

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 64.21  E-value: 7.53e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2163934930  46 MPGGDDRRLKRICDAILRDPADVRTLDAWADEAGASTRTLARLFLAETGISFVHWRQLVRVQHALPLL-ASGMPVAEVSL 124
Cdd:PRK09393  212 VASRESDRLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLLeSSALSIDQIAE 291

                          90       100
                  ....*....|....*....|....*
gi 2163934930 125 ALGYETPGAFAAMFRRVTGTTPSAY 149
Cdd:PRK09393  292 RAGFGSEESLRHHFRRRAATSPAAY 316
 
Name Accession Description Interval E-value
HTH_18 pfam12833
Helix-turn-helix domain;
74-149 1.09e-25

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 93.04  E-value: 1.09e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2163934930  74 WADEAGASTRTLARLFLAETGISFVHWRQLVRVQHALPLLA--SGMPVAEVSLALGYETPGAFAAMFRRVTGTTPSAY 149
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLedTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEY 78
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
70-149 1.00e-23

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 88.38  E-value: 1.00e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2163934930   70 TLDAWADEAGASTRTLARLFLAETGISFVHWRQLVRVQHALPLLASG-MPVAEVSLALGYETPGAFAAMFRRVTGTTPSA 148
Cdd:smart00342   3 TLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTdLSVTEIALRVGFSSQSYFSRAFKKLFGVTPSE 82


                   .
gi 2163934930  149 Y 149
Cdd:smart00342  83 Y 83
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
60-149 8.26e-23

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 90.61  E-value: 8.26e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2163934930  60 AILRDPADVRTLDAWADEAGASTRTLARLFLAETGISFVHWRQLVRVQHALPLLASG-MPVAEVSLALGYETPGAFAAMF 138
Cdd:COG2207   160 LLLLLLLLLLTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETdLSISEIAYELGFSSQSHFSRAF 239

                          90
                  ....*....|.
gi 2163934930 139 RRVTGTTPSAY 149
Cdd:COG2207   240 KKRFGVTPSEY 250
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 43-149 3.76e-22

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: 89.83  E-value: 3.76e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2163934930  43 PLRMPGGDDRRLKRICDAILRDPADVRTLDAWADEAGASTRTLARLFLAETGISFVHWRQLVRVQHALPLL-ASGMPVAE 121
Cdd:COG4977   201 LLVPLGHRDPRLARAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLLeTTDLSIEE 280

                          90       100
                  ....*....|....*....|....*...
gi 2163934930 122 VSLALGYETPGAFAAMFRRVTGTTPSAY 149
Cdd:COG4977   281 IAAACGFGSASHFRRAFRRRFGVSPSAY 308
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 42-149 3.28e-18

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: 79.71  E-value: 3.28e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2163934930  42 HPLRMPG--GDDRRLKRICDAILRDPADVRTLDAWADEAGASTRTLARLFLAETGISFVHWRQLVRVQHALPLLASGMPV 119
Cdd:COG2169    72 RPDLAPGspPRADLVARACRLIEAGAEDRPSLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRARQLLQTGLSV 151

                          90       100       110
                  ....*....|....*....|....*....|
gi 2163934930 120 AEVSLALGYETPGAFAAMFRRVTGTTPSAY 149
Cdd:COG2169   152 TDAAYAAGFGSLSRFYEAFKKLLGMTPSAY 181
ftrA PRK09393
transcriptional activator FtrA; Provisional
 46-149 7.53e-13

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 64.21  E-value: 7.53e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2163934930  46 MPGGDDRRLKRICDAILRDPADVRTLDAWADEAGASTRTLARLFLAETGISFVHWRQLVRVQHALPLL-ASGMPVAEVSL 124
Cdd:PRK09393  212 VASRESDRLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLLeSSALSIDQIAE 291

                          90       100
                  ....*....|....*....|....*
gi 2163934930 125 ALGYETPGAFAAMFRRVTGTTPSAY 149
Cdd:PRK09393  292 RAGFGSEESLRHHFRRRAATSPAAY 316
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
51-149 1.53e-11

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 60.37  E-value: 1.53e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2163934930  51 DRRLKRICDAILRDPADVRTLDAWADEAGASTRTLARLFLAETGISFVHWRQLVRVQHA-LPLLASGMPVAEVSLALGYE 129
Cdd:PRK10572  182 DPRVREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRAkLLLQTTRMPIATIGRNVGYD 261

                          90       100
                  ....*....|....*....|
gi 2163934930 130 TPGAFAAMFRRVTGTTPSAY 149
Cdd:PRK10572  262 DQLYFSRVFKKCTGASPSEF 281
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
71-153 1.02e-09

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 55.45  E-value: 1.02e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2163934930  71 LDAWADEAGASTRTLARLFLAETGISFVHWRQLVRVQHALPLLA-SGMPVAEVSLALGYETPGAFAAMFRRVTGTTPSAY 149
Cdd:PRK13502  195 LDAFCQQEQCSERVLRQQFRAQTGMTINQYLRQVRICHAQYLLQhSPLMISEISMQCGFEDSNYFSVVFTRETGMTPSQW 274


                  ....
gi 2163934930 150 FSLS 153
Cdd:PRK13502  275 RHLS 278
PRK13500 PRK13500
HTH-type transcriptional activator RhaR;
51-153 1.20e-09

HTH-type transcriptional activator RhaR;


Pssm-ID: 184091 [Multi-domain]  Cd Length: 312  Bit Score: 55.49  E-value: 1.20e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2163934930  51 DRRLKRICdAILRDPAdvrTLDAWADEAGASTRTLARLFLAETGISFVHWRQLVRVQHALPLLA-SGMPVAEVSLALGYE 129
Cdd:PRK13500  209 DKLITRLA-ASLKSPF---ALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQhSRLLISDISTECGFE 284

                          90       100
                  ....*....|....*....|....
gi 2163934930 130 TPGAFAAMFRRVTGTTPSAYFSLS 153
Cdd:PRK13500  285 DSNYFSVVFTRETGMTPSQWRHLN 308
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
16-149 8.02e-08

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 49.90  E-value: 8.02e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2163934930  16 PLDSELTGRDGLVIAHLLAEIEWVPGHPLRMPGGDdrRLKRICDAILRDPADVRTLDAWADEAGASTRTLARLFLAETGI 95
Cdd:PRK13501  142 SWSIQLTEVLLLQLAIVLKRHRYRAEQAHLLPDGE--QLDLIMSALQQSLGAYFDMADFCHKNQLVERSLKQLFRQQTGM 219

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2163934930  96 SFVHWRQLVRVQHALPLL-ASGMPVAEVSLALGYETPGAFAAMFRRVTGTTPSAY 149
Cdd:PRK13501  220 SISHYLRQIRLCHAKCLLrGSEHRISDIAARCGFEDSNYFSAVFTREAGMTPRDY 274
PRK15185 PRK15185
transcriptional regulator HilD; Provisional
 56-149 1.14e-05

transcriptional regulator HilD; Provisional


Pssm-ID: 185107 [Multi-domain]  Cd Length: 309  Bit Score: 43.83  E-value: 1.14e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2163934930  56 RICDAILRDPADVRTLDAWADEAGASTRTLARLfLAETGISFVHWRQLVRVQHALPLLASG-MPVAEVSLALGYETPGAF 134
Cdd:PRK15185  210 RVYNIISSSPSRQWKLTDVADHIFMSTSTLKRK-LAEEGTSFSDIYLSARMNQAAKLLRIGnHNVNAVALKCGYDSTSYF 288

                          90
                  ....*....|....*
gi 2163934930 135 AAMFRRVTGTTPSAY 149
Cdd:PRK15185  289 IQCFKKYFKTTPSTF 303
PRK10219 PRK10219
superoxide response transcriptional regulator SoxS;
70-149 2.13e-04

superoxide response transcriptional regulator SoxS;


Pssm-ID: 182314 [Multi-domain]  Cd Length: 107  Bit Score: 38.75  E-value: 2.13e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2163934930  70 TLDAWADEAGASTRTLARLFLA---ETGISFVHWRQLVRVQHALPllASGMPVAEVSLALGYETPGAFAAMFRRVTGTTP 146
Cdd:PRK10219   23 NIDVVAKKSGYSKWYLQRMFRTvthQTLGDYIRQRRLLLAAVELR--TTERPIFDIAMDLGYVSQQTFSRVFRRQFDRTP 100


                  ...
gi 2163934930 147 SAY 149
Cdd:PRK10219  101 SDY 103
PRK15435 PRK15435
bifunctional DNA-binding transcriptional regulator/O6-methylguanine-DNA methyltransferase Ada;
47-149 4.63e-04

bifunctional DNA-binding transcriptional regulator/O6-methylguanine-DNA methyltransferase Ada;


Pssm-ID: 185333 [Multi-domain]  Cd Length: 353  Bit Score: 39.01  E-value: 4.63e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2163934930  47 PGGDD---RRLKRI---CDAILRDPAdvRTLDAWADEAGASTRTLARLFLAETGISFVHWRQLVRVQHALPLLASGMPVA 120
Cdd:PRK15435   74 PDKANpqqHRLDKIthaCRLLEQETP--VTLEALADQVAMSPFHLHRLFKATTGMTPKAWQQAWRARRLREALAKGESVT 151

                          90       100
                  ....*....|....*....|....*....
gi 2163934930 121 EVSLALGYETPGAFAAMFRRVTGTTPSAY 149
Cdd:PRK15435  152 TSILNAGFPDSSSYYRKADETLGMTAKQF 180
PRK09978 PRK09978
DNA-binding transcriptional regulator GadX; Provisional
 56-149 4.83e-04

DNA-binding transcriptional regulator GadX; Provisional


Pssm-ID: 137624 [Multi-domain]  Cd Length: 274  Bit Score: 39.14  E-value: 4.83e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2163934930  56 RICDAILRDPADVRTLDAWADEAGASTRTLARLfLAETGISFVHWRQLVRVQHALPLLA-SGMPVAEVSLALGYETPGAF 134
Cdd:PRK09978  146 RVCTVINNNIAHEWTLARIASELLMSPSLLKKK-LREEETSYSQLLTECRMQRALQLIViHGFSIKRVAVSCGYHSVSYF 224

                          90
                  ....*....|....*
gi 2163934930 135 AAMFRRVTGTTPSAY 149
Cdd:PRK09978  225 IYVFRNYYGMTPTEY 239
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 113-149 5.24e-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: 33.28  E-value: 5.24e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 2163934930 113 LASGMPVAEVSLALGYeTPGAFAAMFRRVTGTTPSAY 149
Cdd:pfam00165   5 LSTNLTIADIADELGF-SRSYFSRLFKKYTGVTPSQY 40
PRK15044 PRK15044
transcriptional regulator SirC; Provisional
 44-149 7.66e-03

transcriptional regulator SirC; Provisional


Pssm-ID: 185004 [Multi-domain]  Cd Length: 295  Bit Score: 35.39  E-value: 7.66e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2163934930  44 LRMPGGDD---RRLK-----RICDAILRDPADVRTLDAWADEAGASTRTLARLFLAETgISFVHWRQLVRVQHALPLLAS 115
Cdd:PRK15044  176 VRKPGGFDfleRAIKittkeKVYNIIISDLTRKWSQAEVAGKLFMSVSSLKRKLAAEE-VSFSKIYLDARMNQAIKLLRM 254

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2163934930 116 GM-PVAEVSLALGYETPGAFAAMFRRVTGTTPSAY 149
Cdd:PRK15044  255 GAgNISQVATMCGYDTPSYFIAIFKRHFKITPLSF 289
 
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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