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Conserved domains on  [gi|495137311|ref|WP_007862119|]
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helix-turn-helix domain-containing protein, partial [Acidovorax sp. CF316]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK09685 super family cl35885
DNA-binding transcriptional activator FeaR; Provisional
 9-51 1.04e-14

DNA-binding transcriptional activator FeaR; Provisional


The actual alignment was detected with superfamily member PRK09685:

Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 65.82  E-value: 1.04e-14
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 495137311   9 LDARRAKASVAEIAFGWGFNDAAHFSRAFKERFGQAPREWRAQ 51
Cdd:PRK09685 258 LRPAADDEKITSIAYKWGFSDSSHFSTAFKQRFGVSPGEYRRK 300
 
Name Accession Description Interval E-value
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 9-51 1.04e-14

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 65.82  E-value: 1.04e-14
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 495137311   9 LDARRAKASVAEIAFGWGFNDAAHFSRAFKERFGQAPREWRAQ 51
Cdd:PRK09685 258 LRPAADDEKITSIAYKWGFSDSSHFSTAFKQRFGVSPGEYRRK 300
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
6-53 1.42e-12

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 59.79  E-value: 1.42e-12
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 495137311   6 RELLdaRRAKASVAEIAFGWGFNDAAHFSRAFKERFGQAPREWRAQGA 53
Cdd:COG2207  210 KRLL--AETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSEYRKRLR 255
HTH_18 pfam12833
Helix-turn-helix domain;
6-51 3.82e-12

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 55.29  E-value: 3.82e-12
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 495137311   6 RELLdARRAKASVAEIAFGWGFNDAAHFSRAFKERFGQAPREWRAQ 51
Cdd:pfam12833 37 RRLL-LEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRRR 81
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
6-49 4.96e-12

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 54.87  E-value: 4.96e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 495137311    6 RELLdaRRAKASVAEIAFGWGFNDAAHFSRAFKERFGQAPREWR 49
Cdd:smart00342 43 RRLL--RDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTPSEYR 84
 
Name Accession Description Interval E-value
PRK09685 PRK09685
DNA-binding transcriptional activator FeaR; Provisional
 9-51 1.04e-14

DNA-binding transcriptional activator FeaR; Provisional


Pssm-ID: 236612 [Multi-domain]  Cd Length: 302  Bit Score: 65.82  E-value: 1.04e-14
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 495137311   9 LDARRAKASVAEIAFGWGFNDAAHFSRAFKERFGQAPREWRAQ 51
Cdd:PRK09685 258 LRPAADDEKITSIAYKWGFSDSSHFSTAFKQRFGVSPGEYRRK 300
AraC COG2207
AraC-type DNA-binding domain and AraC-containing proteins [Transcription];
6-53 1.42e-12

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


Pssm-ID: 441809 [Multi-domain]  Cd Length: 258  Bit Score: 59.79  E-value: 1.42e-12
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 495137311   6 RELLdaRRAKASVAEIAFGWGFNDAAHFSRAFKERFGQAPREWRAQGA 53
Cdd:COG2207  210 KRLL--AETDLSISEIAYELGFSSQSHFSRAFKKRFGVTPSEYRKRLR 255
HTH_18 pfam12833
Helix-turn-helix domain;
6-51 3.82e-12

Helix-turn-helix domain;


Pssm-ID: 432818 [Multi-domain]  Cd Length: 81  Bit Score: 55.29  E-value: 3.82e-12
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 495137311   6 RELLdARRAKASVAEIAFGWGFNDAAHFSRAFKERFGQAPREWRAQ 51
Cdd:pfam12833 37 RRLL-LEDTGLSVAEIALALGFSDASHFSRAFRRLFGLTPSEYRRR 81
HTH_ARAC smart00342
helix_turn_helix, arabinose operon control protein;
6-49 4.96e-12

helix_turn_helix, arabinose operon control protein;


Pssm-ID: 197666 [Multi-domain]  Cd Length: 84  Bit Score: 54.87  E-value: 4.96e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 495137311    6 RELLdaRRAKASVAEIAFGWGFNDAAHFSRAFKERFGQAPREWR 49
Cdd:smart00342 43 RRLL--RDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTPSEYR 84
GlxA COG4977
Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...
 4-58 8.98e-10

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: 52.08  E-value: 8.98e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 495137311   4 ASRELLdaRRAKASVAEIAFGWGFNDAAHFSRAFKERFGQAPREWRAQGATTAAP 58
Cdd:COG4977  266 RARRLL--ETTDLSIEEIAAACGFGSASHFRRAFRRRFGVSPSAYRRRFRARAAA 318
PRK13503 PRK13503
HTH-type transcriptional activator RhaS;
8-51 8.48e-09

HTH-type transcriptional activator RhaS;


Pssm-ID: 184094 [Multi-domain]  Cd Length: 278  Bit Score: 49.29  E-value: 8.48e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 495137311   8 LLDARR----AKASVAEIAFGWGFNDAAHFSRAFKERFGQAPREWRAQ 51
Cdd:PRK13503 225 LLKARHllrhSDASVTDIAYRCGFGDSNHFSTLFRREFSWSPRDIRQG 272
HTH_AraC pfam00165
Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...
 17-49 4.72e-07

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: 41.37  E-value: 4.72e-07
                         10        20        30
                 ....*....|....*....|....*....|...
gi 495137311  17 SVAEIAFGWGFnDAAHFSRAFKERFGQAPREWR 49
Cdd:pfam00165 10 TIADIADELGF-SRSYFSRLFKKYTGVTPSQYR 41
AdaA COG2169
Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...
 6-60 1.86e-05

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: 40.04  E-value: 1.86e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 495137311   6 RELLDARRAKA---------SVAEIAFGWGFNDAAHFSRAFKERFGQAPREWRAQGATTAAPPA 60
Cdd:COG2169  130 KAYARARRLLRarqllqtglSVTDAAYAAGFGSLSRFYEAFKKLLGMTPSAYRRGGAGAAIRFA 193
PRK10572 PRK10572
arabinose operon transcriptional regulator AraC;
6-51 4.09e-04

arabinose operon transcriptional regulator AraC;


Pssm-ID: 236717 [Multi-domain]  Cd Length: 290  Bit Score: 36.10  E-value: 4.09e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 495137311   6 REllDAR--RAK-------ASVAEIAFGWGFNDAAHFSRAFKERFGQAPREWRAQ 51
Cdd:PRK10572 232 RE--DQRisRAKlllqttrMPIATIGRNVGYDDQLYFSRVFKKCTGASPSEFRAR 284
PRK15121 PRK15121
MDR efflux pump AcrAB transcriptional activator RobA;
11-52 5.25e-04

MDR efflux pump AcrAB transcriptional activator RobA;


Pssm-ID: 185076 [Multi-domain]  Cd Length: 289  Bit Score: 35.75  E-value: 5.25e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 495137311  11 ARR-AKASVA---------EIAFGWGFNDAAHFSRAFKERFGQAP------REWRAQG 52
Cdd:PRK15121  56 ARRlSKAAVAlrltsrpilDIALQYRFDSQQTFTRAFKKQFAQTPalyrrsPEWSAFG 113
PRK09940 PRK09940
transcriptional regulator YdeO; Provisional
 5-54 1.44e-03

transcriptional regulator YdeO; Provisional


Pssm-ID: 182157 [Multi-domain]  Cd Length: 253  Bit Score: 34.68  E-value: 1.44e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 495137311   5 SRELLDAR--------RAKASVAEIAFGWGFNDAAHFSRAFKERFGQAP----REWRAQGAT 54
Cdd:PRK09940 179 SQILLDARmqhaknliRVEGSVNKIAEQCGYASTSYFIYAFRKHFGNSPkrvsKEYRCQRHT 240
PRK15340 PRK15340
AraC family transcriptional regulator InvF;
5-46 1.63e-03

AraC family transcriptional regulator InvF;


Pssm-ID: 185240  Cd Length: 216  Bit Score: 34.57  E-value: 1.63e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 495137311   5 SRELLDARRAKASVAEIAFGWGFNDAAHFSRAFKERFGQAPR 46
Cdd:PRK15340 164 AQSLLNSVEGHENITQLAVNHGYSSPSHFSSEIKELIGVSPR 205
PRK13501 PRK13501
HTH-type transcriptional activator RhaR;
12-61 2.11e-03

HTH-type transcriptional activator RhaR;


Pssm-ID: 184092 [Multi-domain]  Cd Length: 290  Bit Score: 34.11  E-value: 2.11e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 495137311  12 RRAKASVAEIAFGWGFNDAAHFSRAFKERFGQAPREWRAQGATTAAPPAQ 61
Cdd:PRK13501 238 RGSEHRISDIAARCGFEDSNYFSAVFTREAGMTPRDYRQRFIRSPVLPAK 287
PRK13502 PRK13502
HTH-type transcriptional activator RhaR;
18-49 3.20e-03

HTH-type transcriptional activator RhaR;


Pssm-ID: 184093 [Multi-domain]  Cd Length: 282  Bit Score: 33.87  E-value: 3.20e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 495137311  18 VAEIAFGWGFNDAAHFSRAFKERFGQAPREWR 49
Cdd:PRK13502 244 ISEISMQCGFEDSNYFSVVFTRETGMTPSQWR 275
 
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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