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Conserved domains on  [gi|2126433143|ref|WP_227497735|]
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MULTISPECIES: helix-turn-helix transcriptional regulator [Marinobacter]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 10007659)

helix-turn-helix (HTH) domain-containing protein with an XRE (Xenobiotic Response Element) family HTH domain, binds DNA and may function as a transcriptional regulator

CATH:  1.10.10.10
Gene Ontology:  GO:0003677
PubMed:  15808743|2644244|8831795
SCOP:  4000362

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
14-86 1.17e-16

DNA-binding transcriptional regulator, XRE family [Transcription];


:

Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 67.48  E-value: 1.17e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2126433143 14 MIRFHLKELIADkefaekRRITIGEIAKDTGINRMTLSKIINHPGHSTVTDNIDKLCTYFDCSVEQLITHIKE 86
Cdd:COG3655    1 MIYVKLDELLAE------RGMTKKELAEATGISRATLSRLKNGKAKAVRLDTLEKICKALDCQPGDLLEYVPD 67
 
Name Accession Description Interval E-value
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
14-86 1.17e-16

DNA-binding transcriptional regulator, XRE family [Transcription];


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 67.48  E-value: 1.17e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2126433143 14 MIRFHLKELIADkefaekRRITIGEIAKDTGINRMTLSKIINHPGHSTVTDNIDKLCTYFDCSVEQLITHIKE 86
Cdd:COG3655    1 MIYVKLDELLAE------RGMTKKELAEATGISRATLSRLKNGKAKAVRLDTLEKICKALDCQPGDLLEYVPD 67
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 18-86 4.72e-11

Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to DNA.


Pssm-ID: 433211 [Multi-domain]  Cd Length: 63  Bit Score: 53.31  E-value: 4.72e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2126433143 18 HLKELIADkefaekRRITIGEIAKDTGINRMTLSKIINHPGHSTVTDNIDKLCTYFDCSVEQLITHIKE 86
Cdd:pfam13443  1 KLRKLMAD------RGISKSDLARATGISRATLSRLRKGKPKRVSLDTLDKICDALGCQPGDLLEYVPD 63
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 26-80 7.64e-07

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.


Pssm-ID: 238045 [Multi-domain]  Cd Length: 58  Bit Score: 42.54  E-value: 7.64e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 2126433143 26 KEFAEKRRITIGEIAKDTGINRMTLSKIINhpGHSTVT-DNIDKLCTYFDCSVEQL 80
Cdd:cd00093    5 KELRKEKGLTQEELAEKLGVSRSTISRIEN--GKRNPSlETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
26-80 3.19e-06

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 40.58  E-value: 3.19e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2126433143  26 KEFAEKRRITIGEIAKDTGINRMTLSKIINhpGHSTVT-DNIDKLCTYFDCSVEQL 80
Cdd:smart00530  3 KELREEKGLTQEELAEKLGVSRSTLSRIEN--GKRKPSlETLKKLAKALGVSLDEL 56
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 26-78 2.40e-03

addiction module antidote protein, HigA family; Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair. [Regulatory functions, DNA interactions, Regulatory functions, Protein interactions, Mobile and extrachromosomal element functions, Other]


Pssm-ID: 274228 [Multi-domain]  Cd Length: 78  Bit Score: 33.74  E-value: 2.40e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 2126433143 26 KEFAEKRRITIGEIAKDTGINRMTLSKIINhpGHSTVTDNID-KLCTYFDCSVE 78
Cdd:TIGR02607 11 EEFLEPLGLSVRALAKALGVSRSTLSRIVN--GRAAITADMAlRLAKALGTSPE 62
 
Name Accession Description Interval E-value
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
14-86 1.17e-16

DNA-binding transcriptional regulator, XRE family [Transcription];


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 67.48  E-value: 1.17e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2126433143 14 MIRFHLKELIADkefaekRRITIGEIAKDTGINRMTLSKIINHPGHSTVTDNIDKLCTYFDCSVEQLITHIKE 86
Cdd:COG3655    1 MIYVKLDELLAE------RGMTKKELAEATGISRATLSRLKNGKAKAVRLDTLEKICKALDCQPGDLLEYVPD 67
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 18-86 4.72e-11

Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to DNA.


Pssm-ID: 433211 [Multi-domain]  Cd Length: 63  Bit Score: 53.31  E-value: 4.72e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2126433143 18 HLKELIADkefaekRRITIGEIAKDTGINRMTLSKIINHPGHSTVTDNIDKLCTYFDCSVEQLITHIKE 86
Cdd:pfam13443  1 KLRKLMAD------RGISKSDLARATGISRATLSRLRKGKPKRVSLDTLDKICDALGCQPGDLLEYVPD 63
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 26-80 7.64e-07

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.


Pssm-ID: 238045 [Multi-domain]  Cd Length: 58  Bit Score: 42.54  E-value: 7.64e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 2126433143 26 KEFAEKRRITIGEIAKDTGINRMTLSKIINhpGHSTVT-DNIDKLCTYFDCSVEQL 80
Cdd:cd00093    5 KELRKEKGLTQEELAEKLGVSRSTISRIEN--GKRNPSlETLEKLAKALGVSLDEL 58
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
26-95 1.94e-06

Transcriptional regulator, contains XRE-family HTH domain [Transcription];


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 41.91  E-value: 1.94e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2126433143 26 KEFAEKRRITIGEIAKDTGINRMTLSKIINhpGHSTVT-DNIDKLCTYFDCSVEQLITHIKEVSDESEGSE 95
Cdd:COG1396   13 RELRKARGLTQEELAERLGVSRSTISRIER--GRRNPSlETLLKLAKALGVSLDELLGGADEELPEALLSE 81
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
26-80 3.19e-06

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 40.58  E-value: 3.19e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2126433143  26 KEFAEKRRITIGEIAKDTGINRMTLSKIINhpGHSTVT-DNIDKLCTYFDCSVEQL 80
Cdd:smart00530  3 KELREEKGLTQEELAEKLGVSRSTLSRIEN--GKRKPSlETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 26-80 1.37e-04

Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteriztic of the whole family.


Pssm-ID: 460181 [Multi-domain]  Cd Length: 55  Bit Score: 36.36  E-value: 1.37e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 2126433143 26 KEFAEKRRITIGEIAKDTGINRMTLSKIINhpGHSTVT-DNIDKLCTYFDCSVEQL 80
Cdd:pfam01381  2 KELREELGLSQEELAEKLGVSRSTISKIEN--GKREPSlETLKKLAEALGVSLDEL 55
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 12-78 2.79e-04

Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense mechanisms];


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 36.33  E-value: 2.79e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2126433143 12 REMIRFHLKELIADkEFAEKRRITIGEIAKDTGINRMTLSKIINhpGHSTVTDNID-KLCTYFDCSVE 78
Cdd:COG3093    2 NKRNPIHPGEILRE-EFLEPLGLSQTELAKALGVSRQRISEILN--GKRAITADTAlRLARAFGTSAE 66
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 26-78 2.40e-03

addiction module antidote protein, HigA family; Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair. [Regulatory functions, DNA interactions, Regulatory functions, Protein interactions, Mobile and extrachromosomal element functions, Other]


Pssm-ID: 274228 [Multi-domain]  Cd Length: 78  Bit Score: 33.74  E-value: 2.40e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 2126433143 26 KEFAEKRRITIGEIAKDTGINRMTLSKIINhpGHSTVTDNID-KLCTYFDCSVE 78
Cdd:TIGR02607 11 EEFLEPLGLSVRALAKALGVSRSTLSRIVN--GRAAITADMAlRLAKALGTSPE 62
HTH_10 pfam04967
HTH DNA binding domain;
28-55 2.72e-03

HTH DNA binding domain;


Pssm-ID: 282780 [Multi-domain]  Cd Length: 53  Bit Score: 32.97  E-value: 2.72e-03
                         10        20
                 ....*....|....*....|....*...
gi 2126433143 28 FAEKRRITIGEIAKDTGINRMTLSKIIN 55
Cdd:pfam04967 18 FDYPRRVTLKELAKELGISKSTLSEHLR 45
 
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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