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Conserved domains on  [gi|1274906969|gb|ATR93327|]
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AraC family transcriptional regulator [Porphyromonas gingivalis]

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];
150-310 7.51e-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: 7.51e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274906969 150 DFLTATLDLIRNTLQNGGRHQEEIVIYLISSLFLFLDDMIADEAEKDCKHTRSETICRDFLLLVSEHHKEQHTVKFYADR 229
Cdd:COG2207    98 LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTLEELARE 177

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274906969 230 LCLSSKHLALTIKTVMGQSASKVINSFIIQQAKSLLRYTDKTVQEIGYELNFSTQSFFGKYFKQHTGMSPGEYRSQEARN 309
Cdd:COG2207   178 LGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSEYRKRLRAR 257


                  .
gi 1274906969 310 R 310
Cdd:COG2207   258 A 258
 
Name Accession Description Interval E-value
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
150-310 7.51e-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: 7.51e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274906969 150 DFLTATLDLIRNTLQNGGRHQEEIVIYLISSLFLFLDDMIADEAEKDCKHTRSETICRDFLLLVSEHHKEQHTVKFYADR 229
Cdd:COG2207    98 LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTLEELARE 177

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274906969 230 LCLSSKHLALTIKTVMGQSASKVINSFIIQQAKSLLRYTDKTVQEIGYELNFSTQSFFGKYFKQHTGMSPGEYRSQEARN 309
Cdd:COG2207   178 LGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSEYRKRLRAR 257


                  .
gi 1274906969 310 R 310
Cdd:COG2207   258 A 258
HTH_18 pfam12833
Helix-turn-helix domain;
226-305 3.20e-19

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 80.33  E-value: 3.20e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274906969 226 YADRLCLSSKHLALTIKTVMGQSASKVINSFIIQQAKSLL-RYTDKTVQEIGYELNFSTQSFFGKYFKQHTGMSPGEYRS 304
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLlEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80


                  .
gi 1274906969 305 Q 305
Cdd:pfam12833  81 R 81
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
220-303 6.40e-18

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 76.82  E-value: 6.40e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274906969  220 QHTVKFYADRLCLSSKHLALTIKTVMGQSASKVINSFIIQQAKSLLRYTDKTVQEIGYELNFSTQSFFGKYFKQHTGMSP 299
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 1274906969  300 GEYR 303
Cdd:smart00342  81 SEYR 84
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
159-308 1.07e-10

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 61.14  E-value: 1.07e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274906969 159 IRNTLQNGGRHQEEIVIYLISSLFLFLDDMIADEAEKDCKHtRSETICRdfllLVSEHHKEQHTVKFYADRLCLSSKHLA 238
Cdd:PRK10572  143 IEQAGQSEGRYSELLAMNLLERLLLRCMEAIPESLHPPMDP-RVREACQ----YISDHLASEFDIESVAQHVCLSPSRLA 217

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274906969 239 LTIKTVMGQSASKVINSFIIQQAKSLLRYTDKTVQEIGYELNFSTQSFFGKYFKQHTGMSPGEYRSQEAR 308
Cdd:PRK10572  218 HLFRQQLGISVLRWREDQRISRAKLLLQTTRMPIATIGRNVGYDDQLYFSRVFKKCTGASPSEFRARCEE 287
 
Name Accession Description Interval E-value
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
150-310 7.51e-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: 7.51e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274906969 150 DFLTATLDLIRNTLQNGGRHQEEIVIYLISSLFLFLDDMIADEAEKDCKHTRSETICRDFLLLVSEHHKEQHTVKFYADR 229
Cdd:COG2207    98 LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTLEELARE 177

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274906969 230 LCLSSKHLALTIKTVMGQSASKVINSFIIQQAKSLLRYTDKTVQEIGYELNFSTQSFFGKYFKQHTGMSPGEYRSQEARN 309
Cdd:COG2207   178 LGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSEYRKRLRAR 257


                  .
gi 1274906969 310 R 310
Cdd:COG2207   258 A 258
HTH_18 pfam12833
Helix-turn-helix domain;
226-305 3.20e-19

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 80.33  E-value: 3.20e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274906969 226 YADRLCLSSKHLALTIKTVMGQSASKVINSFIIQQAKSLL-RYTDKTVQEIGYELNFSTQSFFGKYFKQHTGMSPGEYRS 304
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLlEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRR 80


                  .
gi 1274906969 305 Q 305
Cdd:pfam12833  81 R 81
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
220-303 6.40e-18

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 76.82  E-value: 6.40e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274906969  220 QHTVKFYADRLCLSSKHLALTIKTVMGQSASKVINSFIIQQAKSLLRYTDKTVQEIGYELNFSTQSFFGKYFKQHTGMSP 299
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ....
gi 1274906969  300 GEYR 303
Cdd:smart00342  81 SEYR 84
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 200-310 4.43e-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: 65.56  E-value: 4.43e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274906969 200 TRSETIcRDFLLLVSEHHKEQHTVKFYADRLCLSSKHLALTIKTVMGQSASKVINSFIIQQAKSLLRYTDKTVQEIGYEL 279
Cdd:COG4977   207 HRDPRL-ARAQAWMEANLEEPLSVDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLLETTDLSIEEIAAAC 285

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1274906969 280 NFSTQSFFGKYFKQHTGMSPGEYRSQEARNR 310
Cdd:COG4977   286 GFGSASHFRRAFRRRFGVSPSAYRRRFRARA 316
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
159-308 1.07e-10

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 61.14  E-value: 1.07e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274906969 159 IRNTLQNGGRHQEEIVIYLISSLFLFLDDMIADEAEKDCKHtRSETICRdfllLVSEHHKEQHTVKFYADRLCLSSKHLA 238
Cdd:PRK10572  143 IEQAGQSEGRYSELLAMNLLERLLLRCMEAIPESLHPPMDP-RVREACQ----YISDHLASEFDIESVAQHVCLSPSRLA 217

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274906969 239 LTIKTVMGQSASKVINSFIIQQAKSLLRYTDKTVQEIGYELNFSTQSFFGKYFKQHTGMSPGEYRSQEAR 308
Cdd:PRK10572  218 HLFRQQLGISVLRWREDQRISRAKLLLQTTRMPIATIGRNVGYDDQLYFSRVFKKCTGASPSEFRARCEE 287
PRK10371 PRK10371
transcriptional regulator MelR;
207-308 1.92e-08

transcriptional regulator MelR;


Pssm-ID: 182416 [Multi-domain]  Cd Length: 302  Bit Score: 54.83  E-value: 1.92e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274906969 207 RDFLLLVSEHHKEQHTVKFYADRLCLSSKHLALTIKTVMGQSASKVINSFIIQQAKSLLRYTDKTVQEIGYELNFSTQSF 286
Cdd:PRK10371  194 SQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRALLSDTDKSILDIALTAGFRSSSR 273

                          90       100
                  ....*....|....*....|....
gi 1274906969 287 FGKYFKQHTGMSPGEYR--SQEAR 308
Cdd:PRK10371  274 FYSTFGKYVGMSPQQYRklSQQRR 297
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 203-310 5.42e-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: 5.42e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274906969 203 ETICRdfllLVSEHHKEQHTVKFYADRLCLSSKHLALTIKTVMGQSASKVINSFIIQQAKSLLRyTDKTVQEIGYELNFS 282
Cdd:COG2169    87 ARACR----LIEAGAEDRPSLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRARQLLQ-TGLSVTDAAYAAGFG 161

                          90       100
                  ....*....|....*....|....*...
gi 1274906969 283 TQSFFGKYFKQHTGMSPGEYRSQEARNR 310
Cdd:COG2169   162 SLSRFYEAFKKLLGMTPSAYRRGGAGAA 189
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
227-305 6.47e-06

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 46.98  E-value: 6.47e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1274906969 227 ADRLCLSSKHLALTIKTVMGQSASKVINSFIIQQAKSLLRYTDKTVQEIGYELNFSTQSFFGKYFKQHTGMSPGEYRSQ 305
Cdd:PRK13503  194 ADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSDASVTDIAYRCGFGDSNHFSTLFRREFSWSPRDIRQG 272
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 269-305 5.22e-05

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 44.25  E-value: 5.22e-05
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1274906969 269 DKTVQEIGYELNFSTQSFFGKYFKQHTGMSPGEYRSQ 305
Cdd:PRK09685  264 DEKITSIAYKWGFSDSSHFSTAFKQRFGVSPGEYRRK 300
PRK10296 PRK10296
DNA-binding transcriptional regulator ChbR; Provisional
 216-303 5.61e-05

DNA-binding transcriptional regulator ChbR; Provisional


Pssm-ID: 182362 [Multi-domain]  Cd Length: 278  Bit Score: 43.98  E-value: 5.61e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274906969 216 HHKEQHTVKFYADRLCLSSK---HLALTIKTVMGQSASKVINSFIIQQAKSLLRYTDKTVQEIGYELNFSTQSFFGKYFK 292
Cdd:PRK10296  181 HDKEQFSESALENMVRLSGKsqeYLTRATRRYYGKTPMQIINEIRINFAKKQLEMTNYSVTDIAFEAGYSSPSLFIKTFK 260

                          90
                  ....*....|.
gi 1274906969 293 QHTGMSPGEYR 303
Cdd:PRK10296  261 KLTSFTPGSYR 271
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
232-305 3.65e-04

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 41.43  E-value: 3.65e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1274906969 232 LSSKHLALTIKTVMGQSASKVINSFIIQQAKSLLRYTDKTVQEIGYELNFSTQSFFGKYFKQHTGMSPGEYRSQ 305
Cdd:PRK13501  204 LVERSLKQLFRQQTGMSISHYLRQIRLCHAKCLLRGSEHRISDIAARCGFEDSNYFSAVFTREAGMTPRDYRQR 277
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 268-303 1.66e-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: 1.66e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1274906969 268 TDKTVQEIGYELNFStQSFFGKYFKQHTGMSPGEYR 303
Cdd:pfam00165   7 TNLTIADIADELGFS-RSYFSRLFKKYTGVTPSQYR 41
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
225-309 2.37e-03

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 38.88  E-value: 2.37e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274906969 225 FYADRLCLSSKHLALTIKTVMGQSASKVINSFIIQ----QAKSLLRYTDKTVQEIGYELNFSTQSFFGKYFKQHTGMSPG 300
Cdd:PRK13502  193 FALDAFCQQEQCSERVLRQQFRAQTGMTINQYLRQvricHAQYLLQHSPLMISEISMQCGFEDSNYFSVVFTRETGMTPS 272


                  ....*....
gi 1274906969 301 EYRSQEARN 309
Cdd:PRK13502  273 QWRHLSNQS 281
 
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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