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Conserved domains on  [gi|2733243373|ref|WP_346062637|]
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helix-turn-helix domain-containing protein [Halomonas salifodinae]

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];
58-270 1.56e-12

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


:

Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 65.96  E-value: 1.56e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2733243373  58 PLRRDARRHPGPAWVDGPSLRTARLGVTADLELLGVRFLPGWGGTLLGEPPERLAEAGLLPAQALRHRALDALHERLQAV 137
Cdd:COG2207    48 LLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLLLLALLALLLLVGLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL 127

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2733243373 138 EGFAARVALLERDLLAWLRHSEAPSPLLGAALEWQRRRQGQGSIAALAEALSVGPRRLQRLFRRQLGLSPKQYARVLRVA 217
Cdd:COG2207   128 LALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLE 207

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2733243373 218 QGRALIKRavGPGALTEAAYAAGYCDQAHFVHDFTAVTGLTPGEYRRHVGRRE 270
Cdd:COG2207   208 RAKRLLAE--TDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSEYRKRLRARA 258
 
Name Accession Description Interval E-value
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
58-270 1.56e-12

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 65.96  E-value: 1.56e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2733243373  58 PLRRDARRHPGPAWVDGPSLRTARLGVTADLELLGVRFLPGWGGTLLGEPPERLAEAGLLPAQALRHRALDALHERLQAV 137
Cdd:COG2207    48 LLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLLLLALLALLLLVGLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL 127

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2733243373 138 EGFAARVALLERDLLAWLRHSEAPSPLLGAALEWQRRRQGQGSIAALAEALSVGPRRLQRLFRRQLGLSPKQYARVLRVA 217
Cdd:COG2207   128 LALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLE 207

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2733243373 218 QGRALIKRavGPGALTEAAYAAGYCDQAHFVHDFTAVTGLTPGEYRRHVGRRE 270
Cdd:COG2207   208 RAKRLLAE--TDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSEYRKRLRARA 258
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
180-263 5.44e-12

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 60.26  E-value: 5.44e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2733243373  180 SIAALAEALSVGPRRLQRLFRRQLGLSPKQYARVLRVAQGRALIKRavGPGALTEAAYAAGYCDQAHFVHDFTAVTGLTP 259
Cdd:smart00342   3 TLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRD--TDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 2733243373  260 GEYR 263
Cdd:smart00342  81 SEYR 84
HTH_18 pfam12833
Helix-turn-helix domain;
184-264 3.86e-11

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 57.98  E-value: 3.86e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2733243373 184 LAEALSVGPRRLQRLFRRQLGLSPKQYARVLRVAQGRALIKRAvGPGALTEAAYAAGYCDQAHFVHDFTAVTGLTPGEYR 263
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLED-TGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYR 79


                  .
gi 2733243373 264 R 264
Cdd:pfam12833  80 R 80
PRK10371 PRK10371
transcriptional regulator MelR;
204-275 5.98e-04

transcriptional regulator MelR;


Pssm-ID: 182416 [Multi-domain]  Cd Length: 302  Bit Score: 40.57  E-value: 5.98e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2733243373 204 GLSPKQYARVLRVAQGRALIK---RAVGPGALTeaayaAGYCDQAHFVHDFTAVTGLTPGEYRRHVGRREASFPG 275
Cdd:PRK10371  233 QLTMKQYITAMRINHVRALLSdtdKSILDIALT-----AGFRSSSRFYSTFGKYVGMSPQQYRKLSQQRRQTFPG 302
 
Name Accession Description Interval E-value
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
58-270 1.56e-12

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 65.96  E-value: 1.56e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2733243373  58 PLRRDARRHPGPAWVDGPSLRTARLGVTADLELLGVRFLPGWGGTLLGEPPERLAEAGLLPAQALRHRALDALHERLQAV 137
Cdd:COG2207    48 LLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLLLLALLALLLLVGLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL 127

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2733243373 138 EGFAARVALLERDLLAWLRHSEAPSPLLGAALEWQRRRQGQGSIAALAEALSVGPRRLQRLFRRQLGLSPKQYARVLRVA 217
Cdd:COG2207   128 LALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLE 207

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2733243373 218 QGRALIKRavGPGALTEAAYAAGYCDQAHFVHDFTAVTGLTPGEYRRHVGRRE 270
Cdd:COG2207   208 RAKRLLAE--TDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSEYRKRLRARA 258
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
180-263 5.44e-12

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 60.26  E-value: 5.44e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2733243373  180 SIAALAEALSVGPRRLQRLFRRQLGLSPKQYARVLRVAQGRALIKRavGPGALTEAAYAAGYCDQAHFVHDFTAVTGLTP 259
Cdd:smart00342   3 TLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRD--TDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 2733243373  260 GEYR 263
Cdd:smart00342  81 SEYR 84
HTH_18 pfam12833
Helix-turn-helix domain;
184-264 3.86e-11

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 57.98  E-value: 3.86e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2733243373 184 LAEALSVGPRRLQRLFRRQLGLSPKQYARVLRVAQGRALIKRAvGPGALTEAAYAAGYCDQAHFVHDFTAVTGLTPGEYR 263
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLED-TGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYR 79


                  .
gi 2733243373 264 R 264
Cdd:pfam12833  80 R 80
DUF6597 pfam20240
Domain of unknown function (DUF6597); This presumed domain is found at the N-terminus of ...
 11-107 7.32e-09

Domain of unknown function (DUF6597); This presumed domain is found at the N-terminus of bacterial transcription factor proteins, suggesting that this may be a regulatory domain that binds to some as yet unknown ligand.


Pssm-ID: 466391  Cd Length: 104  Bit Score: 52.30  E-value: 7.32e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2733243373  11 HQLRPRGPLRHVVQSLWWAKGsvAGPGEGVELLHPDGGLGVVFNFGTPLRRDARRHPgPAWVDGPSLRTARLGVTADLEL 90
Cdd:pfam20240   1 QEYPPSPALAPYVECYWVLEW--DLPEPYTQRVLPDGCVDLIFNLGDAYIRLTDGNR-LVFVYGQMTRPFTLTLTGKGRV 77

                          90
                  ....*....|....*..
gi 2733243373  91 LGVRFLPGWGGTLLGEP 107
Cdd:pfam20240  78 FGVRFRPGAAAPFLGIP 94
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 153-272 9.22e-09

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: 55.16  E-value: 9.22e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2733243373 153 AWLRHSEAPSPLLGAALEWQRRRQGQG-SIAALAEALSVGPRRLQRLFRRQLGLSPKQYARVLRVAQGRALIKRavGPGA 231
Cdd:COG4977   200 PLLVPLGHRDPRLARAQAWMEANLEEPlSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLLET--TDLS 277

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2733243373 232 LTEAAYAAGYCDQAHFVHDFTAVTGLTPGEYRRHVGRREAS 272
Cdd:COG4977   278 IEEIAAACGFGSASHFRRAFRRRFGVSPSAYRRRFRARAAA 318
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 157-274 6.84e-08

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: 52.75  E-value: 6.84e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2733243373 157 HSEAPSPLLGAALEW-QRRRQGQGSIAALAEALSVGPRRLQRLFRRQLGLSPKQYARVLRVAQGRALIKRAvgpGALTEA 235
Cdd:COG2169    78 GSPPRADLVARACRLiEAGAEDRPSLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRARQLLQTG---LSVTDA 154

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2733243373 236 AYAAGYCDQAHFVHDFTAVTGLTPGEYRRHVGRREASFP 274
Cdd:COG2169   155 AYAAGFGSLSRFYEAFKKLLGMTPSAYRRGGAGAAIRFA 193
PRK10371 PRK10371
transcriptional regulator MelR;
204-275 5.98e-04

transcriptional regulator MelR;


Pssm-ID: 182416 [Multi-domain]  Cd Length: 302  Bit Score: 40.57  E-value: 5.98e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2733243373 204 GLSPKQYARVLRVAQGRALIK---RAVGPGALTeaayaAGYCDQAHFVHDFTAVTGLTPGEYRRHVGRREASFPG 275
Cdd:PRK10371  233 QLTMKQYITAMRINHVRALLSdtdKSILDIALT-----AGFRSSSRFYSTFGKYVGMSPQQYRKLSQQRRQTFPG 302
ftrA PRK09393
transcriptional activator FtrA; Provisional
 158-268 2.98e-03

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 38.41  E-value: 2.98e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2733243373 158 SEAPSPLLGAALEWQRRRQGQG-SIAALAEALSVGPRRLQRLFRRQLGLSPKQYARVLRVAQGRALIKRAVGPgaLTEAA 236
Cdd:PRK09393  213 ASRESDRLGPLIDWMRAHLAEPhTVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLLESSALS--IDQIA 290

                          90       100       110
                  ....*....|....*....|....*....|..
gi 2733243373 237 YAAGYCDQAHFVHDFTAVTGLTPGEYRRHVGR 268
Cdd:PRK09393  291 ERAGFGSEESLRHHFRRRAATSPAAYRKRFGR 322
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 232-264 6.07e-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: 34.05  E-value: 6.07e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 2733243373 232 LTEAAYAAGYcDQAHFVHDFTAVTGLTPGEYRR 264
Cdd:pfam00165  11 IADIADELGF-SRSYFSRLFKKYTGVTPSQYRH 42
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 232-264 6.84e-03

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 37.32  E-value: 6.84e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 2733243373 232 LTEAAYAAGYCDQAHFVHDFTAVTGLTPGEYRR 264
Cdd:PRK09685  267 ITSIAYKWGFSDSSHFSTAFKQRFGVSPGEYRR 299
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
204-273 7.56e-03

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 37.19  E-value: 7.56e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2733243373 204 GLSPKQYARVLRVAQGRALIKRAvgPGALTEAAYAAGYCDQAHFVHDFTAVTGLTPGEYRRHVGRREASF 273
Cdd:PRK13501  218 GMSISHYLRQIRLCHAKCLLRGS--EHRISDIAARCGFEDSNYFSAVFTREAGMTPRDYRQRFIRSPVLP 285
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
204-263 7.65e-03

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 37.34  E-value: 7.65e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2733243373 204 GLSPKQYARVLRVAQGRALIKRAvgPGALTEAAYAAGYCDQAHFVHDFTAVTGLTPGEYR 263
Cdd:PRK13502  218 GMTINQYLRQVRICHAQYLLQHS--PLMISEISMQCGFEDSNYFSVVFTRETGMTPSQWR 275
 
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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