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Conserved domains on  [gi|188593718|dbj|BAG32693|]
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probable transcriptional regulator AraC family [Porphyromonas gingivalis ATCC 33277]

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];
147-307 7.00e-22

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


:

Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 92.54  E-value: 7.00e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188593718 147 DFLTATLDLIRNALQNGGRHQEEIVIYLISSLFLFLDDMIADEVEKDCKYTRSETICRDFLLLVSEHHKEQHTVKFYADR 226
Cdd:COG2207   98 LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTLEELARE 177

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188593718 227 LCLSSKHLALTIKTVMGQSASKVINSFIIQQAKSLLRYTDKTVQEIGYELNFSTQSFFGKYFKQHTGMSPGEYRSQEARN 306
Cdd:COG2207  178 LGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSEYRKRLRAR 257


                 .
gi 188593718 307 R 307
Cdd:COG2207  258 A 258
 
Name Accession Description Interval E-value
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
147-307 7.00e-22

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 92.54  E-value: 7.00e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188593718 147 DFLTATLDLIRNALQNGGRHQEEIVIYLISSLFLFLDDMIADEVEKDCKYTRSETICRDFLLLVSEHHKEQHTVKFYADR 226
Cdd:COG2207   98 LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTLEELARE 177

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188593718 227 LCLSSKHLALTIKTVMGQSASKVINSFIIQQAKSLLRYTDKTVQEIGYELNFSTQSFFGKYFKQHTGMSPGEYRSQEARN 306
Cdd:COG2207  178 LGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSEYRKRLRAR 257


                 .
gi 188593718 307 R 307
Cdd:COG2207  258 A 258
HTH_18 pfam12833
Helix-turn-helix domain;
223-302 2.95e-19

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 80.33  E-value: 2.95e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188593718  223 YADRLCLSSKHLALTIKTVMGQSASKVINSFIIQQAKSLL-RYTDKTVQEIGYELNFSTQSFFGKYFKQHTGMSPGEYRS 301
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLlEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80


                  .
gi 188593718  302 Q 302
Cdd:pfam12833  81 R 81
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
217-300 6.30e-18

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 76.82  E-value: 6.30e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188593718   217 QHTVKFYADRLCLSSKHLALTIKTVMGQSASKVINSFIIQQAKSLLRYTDKTVQEIGYELNFSTQSFFGKYFKQHTGMSP 296
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 188593718   297 GEYR 300
Cdd:smart00342  81 SEYR 84
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
156-305 4.87e-10

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 59.22  E-value: 4.87e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188593718 156 IRNALQNGGRHQEEIVIYLISSLFLFLDDMIADEVEKDCKyTRSETICRdfllLVSEHHKEQHTVKFYADRLCLSSKHLA 235
Cdd:PRK10572 143 IEQAGQSEGRYSELLAMNLLERLLLRCMEAIPESLHPPMD-PRVREACQ----YISDHLASEFDIESVAQHVCLSPSRLA 217

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188593718 236 LTIKTVMGQSASKVINSFIIQQAKSLLRYTDKTVQEIGYELNFSTQSFFGKYFKQHTGMSPGEYRSQEAR 305
Cdd:PRK10572 218 HLFRQQLGISVLRWREDQRISRAKLLLQTTRMPIATIGRNVGYDDQLYFSRVFKKCTGASPSEFRARCEE 287
 
Name Accession Description Interval E-value
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
147-307 7.00e-22

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 92.54  E-value: 7.00e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188593718 147 DFLTATLDLIRNALQNGGRHQEEIVIYLISSLFLFLDDMIADEVEKDCKYTRSETICRDFLLLVSEHHKEQHTVKFYADR 226
Cdd:COG2207   98 LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTLEELARE 177

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188593718 227 LCLSSKHLALTIKTVMGQSASKVINSFIIQQAKSLLRYTDKTVQEIGYELNFSTQSFFGKYFKQHTGMSPGEYRSQEARN 306
Cdd:COG2207  178 LGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSEYRKRLRAR 257


                 .
gi 188593718 307 R 307
Cdd:COG2207  258 A 258
HTH_18 pfam12833
Helix-turn-helix domain;
223-302 2.95e-19

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 80.33  E-value: 2.95e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188593718  223 YADRLCLSSKHLALTIKTVMGQSASKVINSFIIQQAKSLL-RYTDKTVQEIGYELNFSTQSFFGKYFKQHTGMSPGEYRS 301
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLlEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80


                  .
gi 188593718  302 Q 302
Cdd:pfam12833  81 R 81
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
217-300 6.30e-18

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 76.82  E-value: 6.30e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188593718   217 QHTVKFYADRLCLSSKHLALTIKTVMGQSASKVINSFIIQQAKSLLRYTDKTVQEIGYELNFSTQSFFGKYFKQHTGMSP 296
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 188593718   297 GEYR 300
Cdd:smart00342  81 SEYR 84
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 197-309 2.66e-12

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: 66.33  E-value: 2.66e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188593718 197 TRSETIcRDFLLLVSEHHKEQHTVKFYADRLCLSSKHLALTIKTVMGQSASKVINSFIIQQAKSLLRYTDKTVQEIGYEL 276
Cdd:COG4977  207 HRDPRL-ARAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLLETTDLSIEEIAAAC 285

                         90       100       110
                 ....*....|....*....|....*....|...
gi 188593718 277 NFSTQSFFGKYFKQHTGMSPGEYRSQEARNRQS 309
Cdd:COG4977  286 GFGSASHFRRAFRRRFGVSPSAYRRRFRARAAA 318
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
156-305 4.87e-10

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 59.22  E-value: 4.87e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188593718 156 IRNALQNGGRHQEEIVIYLISSLFLFLDDMIADEVEKDCKyTRSETICRdfllLVSEHHKEQHTVKFYADRLCLSSKHLA 235
Cdd:PRK10572 143 IEQAGQSEGRYSELLAMNLLERLLLRCMEAIPESLHPPMD-PRVREACQ----YISDHLASEFDIESVAQHVCLSPSRLA 217

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188593718 236 LTIKTVMGQSASKVINSFIIQQAKSLLRYTDKTVQEIGYELNFSTQSFFGKYFKQHTGMSPGEYRSQEAR 305
Cdd:PRK10572 218 HLFRQQLGISVLRWREDQRISRAKLLLQTTRMPIATIGRNVGYDDQLYFSRVFKKCTGASPSEFRARCEE 287
PRK10371 PRK10371
transcriptional regulator MelR;
204-305 1.40e-08

transcriptional regulator MelR;


Pssm-ID: 182416 [Multi-domain]  Cd Length: 302  Bit Score: 55.21  E-value: 1.40e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188593718 204 RDFLLLVSEHHKEQHTVKFYADRLCLSSKHLALTIKTVMGQSASKVINSFIIQQAKSLLRYTDKTVQEIGYELNFSTQSF 283
Cdd:PRK10371 194 SQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRALLSDTDKSILDIALTAGFRSSSR 273

                         90       100
                 ....*....|....*....|....
gi 188593718 284 FGKYFKQHTGMSPGEYR--SQEAR 305
Cdd:PRK10371 274 FYSTFGKYVGMSPQQYRklSQQRR 297
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 200-307 5.30e-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: 53.52  E-value: 5.30e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188593718 200 ETICRdfllLVSEHHKEQHTVKFYADRLCLSSKHLALTIKTVMGQSASKVINSFIIQQAKSLLRyTDKTVQEIGYELNFS 279
Cdd:COG2169   87 ARACR----LIEAGAEDRPSLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRARQLLQ-TGLSVTDAAYAAGFG 161

                         90       100
                 ....*....|....*....|....*...
gi 188593718 280 TQSFFGKYFKQHTGMSPGEYRSQEARNR 307
Cdd:COG2169  162 SLSRFYEAFKKLLGMTPSAYRRGGAGAA 189
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
224-302 5.54e-06

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 46.98  E-value: 5.54e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 188593718 224 ADRLCLSSKHLALTIKTVMGQSASKVINSFIIQQAKSLLRYTDKTVQEIGYELNFSTQSFFGKYFKQHTGMSPGEYRSQ 302
Cdd:PRK13503 194 ADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDASVTDIAYRCGFGDSNHFSTLFRREFSWSPRDIRQG 272
PRK10296 PRK10296
DNA-binding transcriptional regulator ChbR; Provisional
 143-300 2.87e-05

DNA-binding transcriptional regulator ChbR; Provisional


Pssm-ID: 182362 [Multi-domain]  Cd Length: 278  Bit Score: 44.75  E-value: 2.87e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188593718 143 RMEKDFLT------ATLDLIRNALQnggRHQEEIVIYLISSLFLFLDDMIADEVEKDCKYTRSETicrdflllvseHHKE 216
Cdd:PRK10296 119 RTNNAFLTyietviSSLNFRETGLD---EFVELVTFYVINRLRHYREEQVIDDIPQWLKATVEKM-----------HDKE 184

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188593718 217 QHTVKFYADRLCLSSK---HLALTIKTVMGQSASKVINSFIIQQAKSLLRYTDKTVQEIGYELNFSTQSFFGKYFKQHTG 293
Cdd:PRK10296 185 QFSESALENMVRLSGKsqeYLTRATRRYYGKTPMQIINEIRINFAKKQLEMTNYSVTDIAFEAGYSSPSLFIKTFKKLTS 264


                 ....*..
gi 188593718 294 MSPGEYR 300
Cdd:PRK10296 265 FTPGSYR 271
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 266-302 4.73e-05

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 44.25  E-value: 4.73e-05
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 188593718 266 DKTVQEIGYELNFSTQSFFGKYFKQHTGMSPGEYRSQ 302
Cdd:PRK09685 264 DEKITSIAYKWGFSDSSHFSTAFKQRFGVSPGEYRRK 300
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
229-302 3.20e-04

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 41.81  E-value: 3.20e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 188593718 229 LSSKHLALTIKTVMGQSASKVINSFIIQQAKSLLRYTDKTVQEIGYELNFSTQSFFGKYFKQHTGMSPGEYRSQ 302
Cdd:PRK13501 204 LVERSLKQLFRQQTGMSISHYLRQIRLCHAKCLLRGSEHRISDIAARCGFEDSNYFSAVFTREAGMTPRDYRQR 277
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 265-300 1.55e-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: 35.59  E-value: 1.55e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 188593718  265 TDKTVQEIGYELNFStQSFFGKYFKQHTGMSPGEYR 300
Cdd:pfam00165   7 TNLTIADIADELGFS-RSYFSRLFKKYTGVTPSQYR 41
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
222-300 2.17e-03

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 39.27  E-value: 2.17e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188593718 222 FYADRLCLSSKHLALTIKTVMGQSASKVINSFIIQ----QAKSLLRYTDKTVQEIGYELNFSTQSFFGKYFKQHTGMSPG 297
Cdd:PRK13502 193 FALDAFCQQEQCSERVLRQQFRAQTGMTINQYLRQvricHAQYLLQHSPLMISEISMQCGFEDSNYFSVVFTRETGMTPS 272


                 ...
gi 188593718 298 EYR 300
Cdd:PRK13502 273 QWR 275
PRK09978 PRK09978
DNA-binding transcriptional regulator GadX; Provisional
 243-312 9.50e-03

DNA-binding transcriptional regulator GadX; Provisional


Pssm-ID: 137624 [Multi-domain]  Cd Length: 274  Bit Score: 37.21  E-value: 9.50e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 188593718 243 GQSASKVINSFIIQQAKSLLRYTDKTVQEIGYELNFSTQSFFGKYFKQHTGMSPGEY---RSQEARNRQSEES 312
Cdd:PRK09978 183 ETSYSQLLTECRMQRALQLIVIHGFSIKRVAVSCGYHSVSYFIYVFRNYYGMTPTEYqerSAQGLPNRDSAAS 255
 
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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