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Conserved domains on  [gi|786805840|dbj|GAO31906|]
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DNA-binding response regulator, AraC family [Geofilum rubicundum JCM 15548]

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];
1-63 1.78e-17

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


:

Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 72.89  E-value: 1.78e-17
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 786805840   1 MSTSELIRKIRVQKAEQLLLSGKYNITETANLVGLNSISYFRECFKEEYGLSPSEYIKKIMER 63
Cdd:COG2207  195 TSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSEYRKRLRAR 257
 
Name Accession Description Interval E-value
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
1-63 1.78e-17

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 72.89  E-value: 1.78e-17
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 786805840   1 MSTSELIRKIRVQKAEQLLLSGKYNITETANLVGLNSISYFRECFKEEYGLSPSEYIKKIMER 63
Cdd:COG2207  195 TSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSEYRKRLRAR 257
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
1-56 9.27e-16

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 64.50  E-value: 9.27e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 786805840    1 MSTSELIRKIRVQKAEQLLLSGKYNITETANLVGLNSISYFRECFKEEYGLSPSEY 56
Cdd:smart00342 28 TTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTPSEY 83
HTH_18 pfam12833
Helix-turn-helix domain;
1-59 1.22e-13

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 58.76  E-value: 1.22e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 786805840   1 MSTSELIRKIRVQKAEQLLL-SGKYNITETANLVGLNSISYFRECFKEEYGLSPSEYIKK 59
Cdd:pfam12833 22 LSPKEYLRRLRLERARRLLLeDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRRR 81
PRK15185 PRK15185
transcriptional regulator HilD; Provisional
 1-58 4.03e-10

transcriptional regulator HilD; Provisional


Pssm-ID: 185107 [Multi-domain]  Cd Length: 309  Bit Score: 53.08  E-value: 4.03e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 786805840   1 MSTSELIRKI--------------RVQKAEQLLLSGKYNITETANLVGLNSISYFRECFKEEYGLSPSEYIK 58
Cdd:PRK15185 234 MSTSTLKRKLaeegtsfsdiylsaRMNQAAKLLRIGNHNVNAVALKCGYDSTSYFIQCFKKYFKTTPSTFIK 305
 
Name Accession Description Interval E-value
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
1-63 1.78e-17

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 72.89  E-value: 1.78e-17
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 786805840   1 MSTSELIRKIRVQKAEQLLLSGKYNITETANLVGLNSISYFRECFKEEYGLSPSEYIKKIMER 63
Cdd:COG2207  195 TSPKQYLRELRLERAKRLLAETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSEYRKRLRAR 257
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
1-56 9.27e-16

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 64.50  E-value: 9.27e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 786805840    1 MSTSELIRKIRVQKAEQLLLSGKYNITETANLVGLNSISYFRECFKEEYGLSPSEY 56
Cdd:smart00342 28 TTPKQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTPSEY 83
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 1-56 6.40e-14

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: 63.64  E-value: 6.40e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 786805840   1 MSTSELIRKIRVQKAEQLLLSGKYNITETANLVGLNSISYFRECFKEEYGLSPSEY 56
Cdd:COG4977  253 TTPARYLQRLRLERARRLLETTDLSIEEIAAACGFGSASHFRRAFRRRFGVSPSAY 308
HTH_18 pfam12833
Helix-turn-helix domain;
1-59 1.22e-13

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 58.76  E-value: 1.22e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 786805840   1 MSTSELIRKIRVQKAEQLLL-SGKYNITETANLVGLNSISYFRECFKEEYGLSPSEYIKK 59
Cdd:pfam12833 22 LSPKEYLRRLRLERARRLLLeDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRRR 81
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 1-56 2.15e-11

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: 56.60  E-value: 2.15e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 786805840   1 MSTSELIRKIRVQKAEQLLLSGKyNITETANLVGLNSISYFRECFKEEYGLSPSEY 56
Cdd:COG2169  127 VTPKAYARARRLLRARQLLQTGL-SVTDAAYAAGFGSLSRFYEAFKKLLGMTPSAY 181
PRK15185 PRK15185
transcriptional regulator HilD; Provisional
 1-58 4.03e-10

transcriptional regulator HilD; Provisional


Pssm-ID: 185107 [Multi-domain]  Cd Length: 309  Bit Score: 53.08  E-value: 4.03e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 786805840   1 MSTSELIRKI--------------RVQKAEQLLLSGKYNITETANLVGLNSISYFRECFKEEYGLSPSEYIK 58
Cdd:PRK15185 234 MSTSTLKRKLaeegtsfsdiylsaRMNQAAKLLRIGNHNVNAVALKCGYDSTSYFIQCFKKYFKTTPSTFIK 305
PRK09978 PRK09978
DNA-binding transcriptional regulator GadX; Provisional
 2-59 1.13e-08

DNA-binding transcriptional regulator GadX; Provisional


Pssm-ID: 137624 [Multi-domain]  Cd Length: 274  Bit Score: 48.77  E-value: 1.13e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 786805840   2 STSELIRKIRVQKAEQLLLSGKYNITETANLVGLNSISYFRECFKEEYGLSPSEYIKK 59
Cdd:PRK09978 185 SYSQLLTECRMQRALQLIVIHGFSIKRVAVSCGYHSVSYFIYVFRNYYGMTPTEYQER 242
PRK15186 PRK15186
AraC family transcriptional regulator; Provisional
 2-57 5.20e-07

AraC family transcriptional regulator; Provisional


Pssm-ID: 185108 [Multi-domain]  Cd Length: 291  Bit Score: 44.29  E-value: 5.20e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 786805840   2 STSELIRKIRVQKAEQLLLSGKYNITETANLVGLNSISYFRECFKEEYGLSPSEYI 57
Cdd:PRK15186 224 SFSEVYLNARMNKATKLLRNSEYNITRVAYMCGYDSASYFTCVFKKHFKTTPSEFL 279
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
1-63 2.13e-06

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 42.58  E-value: 2.13e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 786805840   1 MSTSELIRKIRVQKAEQLLLSGKYNITETANLVGLNSISYFRECFKEEYGLSPSEYIKKIMER 63
Cdd:PRK13501 219 MSISHYLRQIRLCHAKCLLRGSEHRISDIAARCGFEDSNYFSAVFTREAGMTPRDYRQRFIRS 281
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 20-58 3.16e-06

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: 39.06  E-value: 3.16e-06
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 786805840  20 LSGKYNITETANLVGLnSISYFRECFKEEYGLSPSEYIK 58
Cdd:pfam00165  5 LSTNLTIADIADELGF-SRSYFSRLFKKYTGVTPSQYRH 42
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
10-63 2.62e-05

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 39.38  E-value: 2.62e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 786805840  10 IRVQKAEQLLLSGKYNITETANLVGLnSISYFRECFKEEYGLSPSEYIKKI-MER 63
Cdd:COG2207  155 LLLLLLLLLLLLLLLTLEELARELGL-SPRTLSRLFKEETGTSPKQYLRELrLER 208
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
11-62 3.60e-05

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 38.80  E-value: 3.60e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 786805840  11 RVQKAEQLLLSGKYNITETANLVGLNSISYFRECFKEEYGLSPSEYIKKIME 62
Cdd:PRK10572 236 RISRAKLLLQTTRMPIATIGRNVGYDDQLYFSRVFKKCTGASPSEFRARCEE 287
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
9-55 1.18e-04

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 37.35  E-value: 1.18e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 786805840   9 KIRVQKAEQLLLSGKYNITETANLVGLNSISYFRECFKEEYGLSPSE 55
Cdd:PRK13503 222 RLRLLKARHLLRHSDASVTDIAYRCGFGDSNHFSTLFRREFSWSPRD 268
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
1-56 1.21e-04

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 37.73  E-value: 1.21e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 786805840   1 MSTSELIRKIRVQKAEQLLLSGKYNITETANLVGLNSISYFRECFKEEYGLSPSEY 56
Cdd:PRK13502 219 MTINQYLRQVRICHAQYLLQHSPLMISEISMQCGFEDSNYFSVVFTRETGMTPSQW 274
PRK13500 PRK13500
HTH-type transcriptional activator RhaR;
1-56 1.25e-04

HTH-type transcriptional activator RhaR;


Pssm-ID: 184091 [Multi-domain]  Cd Length: 312  Bit Score: 37.39  E-value: 1.25e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 786805840   1 MSTSELIRKIRVQKAEQLLLSGKYNITETANLVGLNSISYFRECFKEEYGLSPSEY 56
Cdd:PRK13500 249 MTINQYLRQVRVCHAQYLLQHSRLLISDISTECGFEDSNYFSVVFTRETGMTPSQW 304
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
23-63 8.14e-04

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 34.07  E-value: 8.14e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 786805840   23 KYNITETANLVGLnSISYFRECFKEEYGLSPSEYIKKI-MER 63
Cdd:smart00342  1 PLTLEDLAEALGV-SPRHLQRLFKKETGTTPKQYLRDRrLER 41
PRK15044 PRK15044
transcriptional regulator SirC; Provisional
 1-60 1.46e-03

transcriptional regulator SirC; Provisional


Pssm-ID: 185004 [Multi-domain]  Cd Length: 295  Bit Score: 34.62  E-value: 1.46e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 786805840   1 MSTSELIRKIRVQKAEQLLLSGKYNITETANLVGLNSISYFRECFKEEYGLSPSEYIKKI 60
Cdd:PRK15044 234 VSFSKIYLDARMNQAIKLLRMGAGNISQVATMCGYDTPSYFIAIFKRHFKITPLSFMRTM 293
HTH_18 pfam12833
Helix-turn-helix domain;
30-60 3.19e-03

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 32.18  E-value: 3.19e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 786805840  30 ANLVGLnSISYFRECFKEEYGLSPSEYIKKI 60
Cdd:pfam12833  2 AAALGM-SPRTLSRLFKRELGLSPKEYLRRL 31
 
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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