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Conserved domains on  [gi|1942734425|ref|WP_197535985|]
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MULTISPECIES: helix-turn-helix domain-containing protein [Marinobacter]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 12122938)

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

CATH:  1.10.10.10
Gene Ontology:  GO:0003677
PubMed:  10473770|15808743

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_18 pfam12833
Helix-turn-helix domain;
106-182 6.37e-20

Helix-turn-helix domain;


:

Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 79.17  E-value: 6.37e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1942734425 106 LAQHLEISQRHVERLFKHWMEMTPKQYQRILRVKRAINYIREHGQVNLAEVAHQFGFSDQAHMTREFRTIARITPGQ 182
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSE 77
 
Name Accession Description Interval E-value
HTH_18 pfam12833
Helix-turn-helix domain;
106-182 6.37e-20

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 79.17  E-value: 6.37e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1942734425 106 LAQHLEISQRHVERLFKHWMEMTPKQYQRILRVKRAINYIREHGQVNLAEVAHQFGFSDQAHMTREFRTIARITPGQ 182
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSE 77
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
105-182 1.54e-18

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 75.67  E-value: 1.54e-18
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1942734425  105 SLAQHLEISQRHVERLFKHWMEMTPKQYQRILRVKRAINYIReHGQVNLAEVAHQFGFSDQAHMTREFRTIARITPGQ 182
Cdd:smart00342   6 DLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLR-DTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTPSE 82
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
106-182 6.37e-18

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 78.67  E-value: 6.37e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1942734425 106 LAQHLEISQRHVERLFKHWMEMTPKQYQRILRVKRAINYIReHGQVNLAEVAHQFGFSDQAHMTREFRTIARITPGQ 182
Cdd:COG2207   174 LARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLA-ETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSE 249
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 103-182 1.11e-05

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 44.64  E-value: 1.11e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942734425 103 PGSLAQHLEISQRHVERLFKHwMEMTPKQYQRILRVKRAINYIREHGQ-VNLAEVAHQFGFSDQAHMTREFRTIARITPG 181
Cdd:PRK09685  217 PEWIAGELGISVRSLYRLFAE-QGLVVAQYIRNRRLDRCADDLRPAADdEKITSIAYKWGFSDSSHFSTAFKQRFGVSPG 295


                  .
gi 1942734425 182 Q 182
Cdd:PRK09685  296 E 296
 
Name Accession Description Interval E-value
HTH_18 pfam12833
Helix-turn-helix domain;
106-182 6.37e-20

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 79.17  E-value: 6.37e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1942734425 106 LAQHLEISQRHVERLFKHWMEMTPKQYQRILRVKRAINYIREHGQVNLAEVAHQFGFSDQAHMTREFRTIARITPGQ 182
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSE 77
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
105-182 1.54e-18

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 75.67  E-value: 1.54e-18
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1942734425  105 SLAQHLEISQRHVERLFKHWMEMTPKQYQRILRVKRAINYIReHGQVNLAEVAHQFGFSDQAHMTREFRTIARITPGQ 182
Cdd:smart00342   6 DLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLR-DTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTPSE 82
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
106-182 6.37e-18

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 78.67  E-value: 6.37e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1942734425 106 LAQHLEISQRHVERLFKHWMEMTPKQYQRILRVKRAINYIReHGQVNLAEVAHQFGFSDQAHMTREFRTIARITPGQ 182
Cdd:COG2207   174 LARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLA-ETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSE 249
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 89-182 9.84e-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: 67.49  E-value: 9.84e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942734425  89 ALQQALDCIRDD-AEP---GSLAQHLEISQRHVERLFKHWMEMTPKQYQRILRVKRAINYIrEHGQVNLAEVAHQFGFSD 164
Cdd:COG4977   211 RLARAQAWMEANlEEPlsvDELARRAGMSPRTLERRFRAATGTTPARYLQRLRLERARRLL-ETTDLSIEEIAAACGFGS 289

                          90
                  ....*....|....*...
gi 1942734425 165 QAHMTREFRTIARITPGQ 182
Cdd:COG4977   290 ASHFRRAFRRRFGVSPSA 307
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 91-182 5.16e-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: 57.37  E-value: 5.16e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942734425  91 QQALDCIRDDAEP----GSLAQHLEISQRHVERLFKHWMEMTPKQYQRILRVKRAINYIREHGQVnlAEVAHQFGFSDQA 166
Cdd:COG2169    87 ARACRLIEAGAEDrpslEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRARQLLQTGLSV--TDAAYAAGFGSLS 164

                          90
                  ....*....|....*.
gi 1942734425 167 HMTREFRTIARITPGQ 182
Cdd:COG2169   165 RFYEAFKKLLGMTPSA 180
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 103-182 1.11e-05

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 44.64  E-value: 1.11e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942734425 103 PGSLAQHLEISQRHVERLFKHwMEMTPKQYQRILRVKRAINYIREHGQ-VNLAEVAHQFGFSDQAHMTREFRTIARITPG 181
Cdd:PRK09685  217 PEWIAGELGISVRSLYRLFAE-QGLVVAQYIRNRRLDRCADDLRPAADdEKITSIAYKWGFSDSSHFSTAFKQRFGVSPG 295


                  .
gi 1942734425 182 Q 182
Cdd:PRK09685  296 E 296
ftrA PRK09393
transcriptional activator FtrA; Provisional
 90-182 1.14e-05

transcriptional activator FtrA; Provisional


Pssm-ID: 181818 [Multi-domain]  Cd Length: 322  Bit Score: 44.57  E-value: 1.14e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942734425  90 LQQALDCIRDD-AEP---GSLAQHLEISQRHVERLFKHWMEMTPKQYQRILRVKRAINYIrEHGQVNLAEVAHQFGFSDQ 165
Cdd:PRK09393  220 LGPLIDWMRAHlAEPhtvASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLL-ESSALSIDQIAERAGFGSE 298

                          90
                  ....*....|....*..
gi 1942734425 166 AHMTREFRTIARITPGQ 182
Cdd:PRK09393  299 ESLRHHFRRRAATSPAA 315
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 104-134 3.01e-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: 3.01e-05
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1942734425 104 GSLAQHLEISQRHVERLFKHWMEMTPKQYQR 134
Cdd:pfam00165  12 ADIADELGFSRSYFSRLFKKYTGVTPSQYRH 42
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
64-173 7.81e-05

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 41.97  E-value: 7.81e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942734425  64 NNVSRVSTMQSWAENNFRltrlipgalqqaldcirDDAEPGSLAQHLEISQRHVERLFKHWMEMTPKQYQRILRVKRAIN 143
Cdd:PRK13503  168 NSDARLNQLLAWLEDHFA-----------------EEVNWEALADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARH 230

                          90       100       110
                  ....*....|....*....|....*....|
gi 1942734425 144 YIReHGQVNLAEVAHQFGFSDQAHMTREFR 173
Cdd:PRK13503  231 LLR-HSDASVTDIAYRCGFGDSNHFSTLFR 259
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
108-182 4.73e-04

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 39.65  E-value: 4.73e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1942734425 108 QHLEISQRHVERLFKHWMEMTPKQYQRILRVKRAiNYIREHGQVNLAEVAHQFGFSDQAHMTREFRTIARITPGQ 182
Cdd:PRK13502  200 QQEQCSERVLRQQFRAQTGMTINQYLRQVRICHA-QYLLQHSPLMISEISMQCGFEDSNYFSVVFTRETGMTPSQ 273
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
85-180 5.03e-03

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 36.42  E-value: 5.03e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942734425  85 LIPGALQQALDCIRDDAEpgsLAQHLEISQRHVERLFKHWMEMTPKQYQRILRVKRAiNYIREHGQVNLAEVAHQFGFSD 164
Cdd:PRK13501  180 LIMSALQQSLGAYFDMAD---FCHKNQLVERSLKQLFRQQTGMSISHYLRQIRLCHA-KCLLRGSEHRISDIAARCGFED 255

                          90
                  ....*....|....*.
gi 1942734425 165 QAHMTREFRTIARITP 180
Cdd:PRK13501  256 SNYFSAVFTREAGMTP 271
PRK15435 PRK15435
bifunctional DNA-binding transcriptional regulator/O6-methylguanine-DNA methyltransferase Ada;
105-182 5.07e-03

bifunctional DNA-binding transcriptional regulator/O6-methylguanine-DNA methyltransferase Ada;


Pssm-ID: 185333 [Multi-domain]  Cd Length: 353  Bit Score: 36.69  E-value: 5.07e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1942734425 105 SLAQHLEISQRHVERLFKHWMEMTPKQYQRILRVKRAINYIREHGQVNLAEVAHqfGFSDQAHMTREFRTIARITPGQ 182
Cdd:PRK15435  104 ALADQVAMSPFHLHRLFKATTGMTPKAWQQAWRARRLREALAKGESVTTSILNA--GFPDSSSYYRKADETLGMTAKQ 179
PRK13500 PRK13500
HTH-type transcriptional activator RhaR;
113-182 7.14e-03

HTH-type transcriptional activator RhaR;


Pssm-ID: 184091 [Multi-domain]  Cd Length: 312  Bit Score: 36.23  E-value: 7.14e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942734425 113 SQRHVERLFKHWMEMTPKQYQRILRVKRAiNYIREHGQVNLAEVAHQFGFSDQAHMTREFRTIARITPGQ 182
Cdd:PRK13500  235 SERVLRQQFRQQTGMTINQYLRQVRVCHA-QYLLQHSRLLISDISTECGFEDSNYFSVVFTRETGMTPSQ 303
 
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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