NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|506367959|ref|WP_015887678|]
View 

helix-turn-helix domain-containing protein [Sinorhizobium fredii]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 1000956)

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

Gene Ontology:  GO:0003677
PubMed:  15808743

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
GlxA super family cl34854
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 168-298 1.61e-19

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


The actual alignment was detected with superfamily member COG4977:

Pssm-ID: 444002 [Multi-domain]  Cd Length: 318  Bit Score: 86.75  E-value: 1.61e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506367959 168 HIAIAICAHLLHaygDPDQPGSSSTRLSVWQEKAAKD--------FMIDHFADQFSMAAAASAAGVSTRRFIAGFKGVTG 239
Cdd:COG4977  176 ELANAVARRLVV---DPRRPGGQAQFSPLLVPLGHRDprlaraqaWMEANLEEPLSVDELARRAGMSPRTLERRFRAATG 252

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 506367959 240 QTPQQWLLGYRTARAKQYLGEHSLTVPEIATRCGFTDENHFITGFRRVTGSTPGAWRAR 298
Cdd:COG4977  253 TTPARYLQRLRLERARRLLETTDLSIEEIAAACGFGSASHFRRAFRRRFGVSPSAYRRR 311
 
Name Accession Description Interval E-value
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 168-298 1.61e-19

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: 86.75  E-value: 1.61e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506367959 168 HIAIAICAHLLHaygDPDQPGSSSTRLSVWQEKAAKD--------FMIDHFADQFSMAAAASAAGVSTRRFIAGFKGVTG 239
Cdd:COG4977  176 ELANAVARRLVV---DPRRPGGQAQFSPLLVPLGHRDprlaraqaWMEANLEEPLSVDELARRAGMSPRTLERRFRAATG 252

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 506367959 240 QTPQQWLLGYRTARAKQYLGEHSLTVPEIATRCGFTDENHFITGFRRVTGSTPGAWRAR 298
Cdd:COG4977  253 TTPARYLQRLRLERARRLLETTDLSIEEIAAACGFGSASHFRRAFRRRFGVSPSAYRRR 311
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
224-296 6.65e-19

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 79.52  E-value: 6.65e-19
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 506367959   224 GVSTRRFIAGFKGVTGQTPQQWLLGYRTARAKQYLGEHSLTVPEIATRCGFTDENHFITGFRRVTGSTPGAWR 296
Cdd:smart00342  12 GVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTPSEYR 84
HTH_18 pfam12833
Helix-turn-helix domain;
224-298 7.58e-19

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 79.17  E-value: 7.58e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 506367959  224 GVSTRRFIAGFKGVTGQTPQQWLLGYRTARAKQYLGEHS-LTVPEIATRCGFTDENHFITGFRRVTGSTPGAWRAR 298
Cdd:pfam12833   6 GMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEDTgLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRRR 81
ftrA PRK09393
transcriptional activator FtrA; Provisional
 204-298 9.21e-15

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 73.46  E-value: 9.21e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506367959 204 DFMIDHFADQFSMAAAASAAGVSTRRFIAGFKGVTGQTPQQWLLGYRTARAKQYLGEHSLTVPEIATRCGFTDENHFITG 283
Cdd:PRK09393 225 DWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLLESSALSIDQIAERAGFGSEESLRHH 304

                         90
                 ....*....|....*
gi 506367959 284 FRRVTGSTPGAWRAR 298
Cdd:PRK09393 305 FRRRAATSPAAYRKR 319
 
Name Accession Description Interval E-value
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 168-298 1.61e-19

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: 86.75  E-value: 1.61e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506367959 168 HIAIAICAHLLHaygDPDQPGSSSTRLSVWQEKAAKD--------FMIDHFADQFSMAAAASAAGVSTRRFIAGFKGVTG 239
Cdd:COG4977  176 ELANAVARRLVV---DPRRPGGQAQFSPLLVPLGHRDprlaraqaWMEANLEEPLSVDELARRAGMSPRTLERRFRAATG 252

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 506367959 240 QTPQQWLLGYRTARAKQYLGEHSLTVPEIATRCGFTDENHFITGFRRVTGSTPGAWRAR 298
Cdd:COG4977  253 TTPARYLQRLRLERARRLLETTDLSIEEIAAACGFGSASHFRRAFRRRFGVSPSAYRRR 311
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
224-296 6.65e-19

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 79.52  E-value: 6.65e-19
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 506367959   224 GVSTRRFIAGFKGVTGQTPQQWLLGYRTARAKQYLGEHSLTVPEIATRCGFTDENHFITGFRRVTGSTPGAWR 296
Cdd:smart00342  12 GVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTPSEYR 84
HTH_18 pfam12833
Helix-turn-helix domain;
224-298 7.58e-19

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 79.17  E-value: 7.58e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 506367959  224 GVSTRRFIAGFKGVTGQTPQQWLLGYRTARAKQYLGEHS-LTVPEIATRCGFTDENHFITGFRRVTGSTPGAWRAR 298
Cdd:pfam12833   6 GMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEDTgLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRRR 81
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
46-301 1.02e-18

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 83.68  E-value: 1.02e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506367959  46 ASRLVSLPPDEAYFLMLYLKDAYHCDVGPDGTESETRRFRQGSICLVDLANGACIRLSSDLDSLAFQIPRELFREVSEFS 125
Cdd:COG2207   10 LLLLLALLLLLLLLLLLLILLLLALVLLLLLLALLLLLLLLLGLLGGLLLLLLLLLLLGLLLLLLLLLLGLLLLALLALL 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506367959 126 TAPKATRLRCRRGEHDDVMCNLGAALLPLFERQGNSQAPVLQHIAIAICAHLLHAYGDPDQPGSSSTRLSVWQEKAAKDF 205
Cdd:COG2207   90 LLVGLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506367959 206 MIDHFADQFsmaaaasaaGVSTRRFIAGFKGVTGQTPQQWLLGYRTARAKQYLGEHSLTVPEIATRCGFTDENHFITGFR 285
Cdd:COG2207  170 TLEELAREL---------GLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFK 240

                        250
                 ....*....|....*.
gi 506367959 286 RVTGSTPGAWRARWLQ 301
Cdd:COG2207  241 KRFGVTPSEYRKRLRA 256
ftrA PRK09393
transcriptional activator FtrA; Provisional
 204-298 9.21e-15

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 73.46  E-value: 9.21e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506367959 204 DFMIDHFADQFSMAAAASAAGVSTRRFIAGFKGVTGQTPQQWLLGYRTARAKQYLGEHSLTVPEIATRCGFTDENHFITG 283
Cdd:PRK09393 225 DWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLLESSALSIDQIAERAGFGSEESLRHH 304

                         90
                 ....*....|....*
gi 506367959 284 FRRVTGSTPGAWRAR 298
Cdd:PRK09393 305 FRRRAATSPAAYRKR 319
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
155-296 1.82e-11

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 63.53  E-value: 1.82e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506367959 155 FERQGNSQAPVLQHIAIAICAHLL-----HAYGDPDQPGSSSTRL-----SVWQEKAAKDFMIDHFADQFSmaaaasaag 224
Cdd:PRK13502 133 LEHESNGRDPLANEMAELLFGQLVmtlkrHRYATDDLPATSRETLldkliTALANSLECPFALDAFCQQEQ--------- 203

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 506367959 225 VSTRRFIAGFKGVTGQTPQQWLLGYRTARAkQYLGEHS-LTVPEIATRCGFTDENHFITGFRRVTGSTPGAWR 296
Cdd:PRK13502 204 CSERVLRQQFRAQTGMTINQYLRQVRICHA-QYLLQHSpLMISEISMQCGFEDSNYFSVVFTRETGMTPSQWR 275
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
194-301 3.58e-11

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 62.61  E-value: 3.58e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506367959 194 LSVWQEKAAKDFMIDHFADQFSMaaaasaagvSTRRFIAGFKGVTGQTPQQWLLGYRTARAKQYLGEHSLTVPEIATRCG 273
Cdd:PRK13501 182 MSALQQSLGAYFDMADFCHKNQL---------VERSLKQLFRQQTGMSISHYLRQIRLCHAKCLLRGSEHRISDIAARCG 252

                         90       100
                 ....*....|....*....|....*...
gi 506367959 274 FTDENHFITGFRRVTGSTPGAWRARWLQ 301
Cdd:PRK13501 253 FEDSNYFSAVFTREAGMTPRDYRQRFIR 280
PRK13500 PRK13500
HTH-type transcriptional activator RhaR;
155-296 1.57e-10

HTH-type transcriptional activator RhaR;


Pssm-ID: 184091 [Multi-domain]  Cd Length: 312  Bit Score: 60.89  E-value: 1.57e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506367959 155 FERQGNSQAPVLQHIAIAICAHLL-----HAY-GDPDQPGSSSTRLSVWQEKAAKD----FMIDHFADQFSmaaaasaag 224
Cdd:PRK13500 163 LEHESSQHVPFANEMAELLFGQLVmllnrHRYtSDSLPPTSSETLLDKLITRLAASlkspFALDKFCDEAS--------- 233

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 506367959 225 VSTRRFIAGFKGVTGQTPQQWLLGYRTARAkQYLGEHS-LTVPEIATRCGFTDENHFITGFRRVTGSTPGAWR 296
Cdd:PRK13500 234 CSERVLRQQFRQQTGMTINQYLRQVRVCHA-QYLLQHSrLLISDISTECGFEDSNYFSVVFTRETGMTPSQWR 305
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 184-298 3.26e-10

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: 60.07  E-value: 3.26e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506367959 184 PDQ-PGSSSTRLSVwqeKAAKDFMIDHFADQFSMAAAASAAGVSTRRFIAGFKGVTGQTPQQWLLGYRTARAKQYLGEhS 262
Cdd:COG2169   73 PDLaPGSPPRADLV---ARACRLIEAGAEDRPSLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRARQLLQT-G 148

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 506367959 263 LTVPEIATRCGFTDENHFITGFRRVTGSTPGAWRAR 298
Cdd:COG2169  149 LSVTDAAYAAGFGSLSRFYEAFKKLLGMTPSAYRRG 184
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
197-296 2.33e-08

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 53.91  E-value: 2.33e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506367959 197 W-QEKAAKDFMIDHFADQFSMaaaasaagvSTRRFIAGFKGVTGQTPQQWLLGYRTARAKQYLGEHSLTVPEIATRCGFT 275
Cdd:PRK13503 179 WlEDHFAEEVNWEALADQFSL---------SLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDASVTDIAYRCGFG 249

                         90       100
                 ....*....|....*....|.
gi 506367959 276 DENHFITGFRRVTGSTPGAWR 296
Cdd:PRK13503 250 DSNHFSTLFRREFSWSPRDIR 270
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 261-296 5.64e-05

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: 39.83  E-value: 5.64e-05
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 506367959  261 HSLTVPEIATRCGFtDENHFITGFRRVTGSTPGAWR 296
Cdd:pfam00165   7 TNLTIADIADELGF-SRSYFSRLFKKYTGVTPSQYR 41
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
201-298 7.89e-04

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 40.34  E-value: 7.89e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 506367959 201 AAKDFMIDHFADQFSMAAAASAAGVSTRRFIAGFKGVTGQTPQQWLLGYRTARAKQYLGEHSLTVPEIATRCGFTDENHF 280
Cdd:PRK10572 187 EACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRAKLLLQTTRMPIATIGRNVGYDDQLYF 266

                         90
                 ....*....|....*...
gi 506367959 281 ITGFRRVTGSTPGAWRAR 298
Cdd:PRK10572 267 SRVFKKCTGASPSEFRAR 284
PRK10296 PRK10296
DNA-binding transcriptional regulator ChbR; Provisional
 226-298 2.89e-03

DNA-binding transcriptional regulator ChbR; Provisional


Pssm-ID: 182362 [Multi-domain]  Cd Length: 278  Bit Score: 38.58  E-value: 2.89e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 506367959 226 STRRFIagfkgvtGQTPQQWLLGYRTARAKQYLGEHSLTVPEIATRCGFTDENHFITGFRRVTGSTPGAWRAR 298
Cdd:PRK10296 208 ATRRYY-------GKTPMQIINEIRINFAKKQLEMTNYSVTDIAFEAGYSSPSLFIKTFKKLTSFTPGSYRKK 273
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 267-300 3.61e-03

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 38.47  E-value: 3.61e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 506367959 267 EIATRCGFTDENHFITGFRRVTGSTPGAWRARWL 300
Cdd:PRK09685 269 SIAYKWGFSDSSHFSTAFKQRFGVSPGEYRRKFR 302
 
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