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MULTISPECIES: helix-turn-helix transcriptional regulator [Enterobacterales]

Protein Classification

helix-turn-helix transcriptional regulator( domain architecture ID 10787697)

helix-turn-helix (HTH) transcriptional regulator containing a XRE (Xenobiotic Response Element) family HTH domain may act as a transcriptional regulator that controls the expression of genes involved in stress response

CATH:  1.10.10.10
Gene Ontology:  GO:0003677
PubMed:  10473770|2644244
SCOP:  4000362

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
17-68 5.20e-13

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


:

Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 58.32  E-value: 5.20e-13
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 582963866 17 LIGFRKANGLTQKDLSERLGVTQQTYSRLEANPASASIERLFKVFSILGVKI 68
Cdd:COG1476   9 LKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSL 60
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
17-68 5.20e-13

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 58.32  E-value: 5.20e-13
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 582963866 17 LIGFRKANGLTQKDLSERLGVTQQTYSRLEANPASASIERLFKVFSILGVKI 68
Cdd:COG1476   9 LKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSL 60
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
20-70 2.40e-12

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 56.37  E-value: 2.40e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 582963866   20 FRKANGLTQKDLSERLGVTQQTYSRLEANPASASIERLFKVFSILGVKISF 70
Cdd:smart00530  5 LREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDE 55
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 20-70 3.79e-12

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: 56.02  E-value: 3.79e-12
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 582963866 20 FRKANGLTQKDLSERLGVTQQTYSRLEANPASASIERLFKVFSILGVKISF 70
Cdd:cd00093   7 LRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDE 57
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 21-70 5.00e-12

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: 55.62  E-value: 5.00e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 582963866  21 RKANGLTQKDLSERLGVTQQTYSRLEANPASASIERLFKVFSILGVKISF 70
Cdd:pfam01381  5 REELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDE 54
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 21-65 1.00e-07

transcriptional regulator, y4mF family; Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems. [Regulatory functions, DNA interactions]


Pssm-ID: 213767 [Multi-domain]  Cd Length: 58  Bit Score: 44.57  E-value: 1.00e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 582963866  21 RKANGLTQKDLSERLGVTQQTYSRLEANPASASIERLFKVFSILG 65
Cdd:TIGR03070 11 RKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDALG 55
PRK09726 PRK09726
type II toxin-antitoxin system antitoxin HipB;
12-77 1.16e-06

type II toxin-antitoxin system antitoxin HipB;


Pssm-ID: 182049  Cd Length: 88  Bit Score: 42.66  E-value: 1.16e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 582963866 12 QLRPLLIGFRKANGLTQKDLSERLGVTQQTYSRLEANPASASIERLFKVFSILGVKISFSSATTSS 77
Cdd:PRK09726 12 QLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMTLCDAKNAS 77
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
17-68 5.20e-13

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 58.32  E-value: 5.20e-13
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 582963866 17 LIGFRKANGLTQKDLSERLGVTQQTYSRLEANPASASIERLFKVFSILGVKI 68
Cdd:COG1476   9 LKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSL 60
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
20-70 2.40e-12

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 56.37  E-value: 2.40e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 582963866   20 FRKANGLTQKDLSERLGVTQQTYSRLEANPASASIERLFKVFSILGVKISF 70
Cdd:smart00530  5 LREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDE 55
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
21-84 2.90e-12

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 56.93  E-value: 2.90e-12
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 582963866 21 RKANGLTQKDLSERLGVTQQTYSRLEANPASASIERLFKVFSILGVKIS--FSSATTSSERKQTEE 84
Cdd:COG1396  16 RKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDelLGGADEELPEALLSE 81
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 20-70 3.79e-12

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: 56.02  E-value: 3.79e-12
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 582963866 20 FRKANGLTQKDLSERLGVTQQTYSRLEANPASASIERLFKVFSILGVKISF 70
Cdd:cd00093   7 LRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDE 57
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 21-70 5.00e-12

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: 55.62  E-value: 5.00e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 582963866  21 RKANGLTQKDLSERLGVTQQTYSRLEANPASASIERLFKVFSILGVKISF 70
Cdd:pfam01381  5 REELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDE 54
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 20-70 5.17e-11

Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain CBS pair) [Transcription];


Pssm-ID: 442838 [Multi-domain]  Cd Length: 95  Bit Score: 53.87  E-value: 5.17e-11
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 582963866 20 FRKANGLTQKDLSERLGVTQQTYSRLEANPASASIERLFKVFSILGVKISF 70
Cdd:COG3620  25 MRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSA 75
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 21-69 4.21e-08

Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and HTH domains [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441418 [Multi-domain]  Cd Length: 70  Bit Score: 45.70  E-value: 4.21e-08
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 582963866 21 RKANGLTQKDLSERLGVTQQTYSRLEANPASASIERLFKVFSILGVKIS 69
Cdd:COG1813  21 REARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLA 69
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 21-65 1.00e-07

transcriptional regulator, y4mF family; Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems. [Regulatory functions, DNA interactions]


Pssm-ID: 213767 [Multi-domain]  Cd Length: 58  Bit Score: 44.57  E-value: 1.00e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 582963866  21 RKANGLTQKDLSERLGVTQQTYSRLEANPASASIERLFKVFSILG 65
Cdd:TIGR03070 11 RKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDALG 55
PRK09726 PRK09726
type II toxin-antitoxin system antitoxin HipB;
12-77 1.16e-06

type II toxin-antitoxin system antitoxin HipB;


Pssm-ID: 182049  Cd Length: 88  Bit Score: 42.66  E-value: 1.16e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 582963866 12 QLRPLLIGFRKANGLTQKDLSERLGVTQQTYSRLEANPASASIERLFKVFSILGVKISFSSATTSS 77
Cdd:PRK09726 12 QLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMTLCDAKNAS 77
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 12-47 2.68e-05

Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.


Pssm-ID: 433309 [Multi-domain]  Cd Length: 64  Bit Score: 38.66  E-value: 2.68e-05
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 582963866  12 QLRPLLIGFRKANGLTQKDLSERLGVTQQTYSRLEA 47
Cdd:pfam13560  1 ELGARLRRLRERAGLSQEALARRLGVSRSTLSRLET 36
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 21-60 2.86e-05

putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.


Pssm-ID: 274805 [Multi-domain]  Cd Length: 127  Bit Score: 39.54  E-value: 2.86e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 582963866   21 RKANGLTQKDLSERLGVTQQTYSRLE--ANPASASIERLFKV 60
Cdd:TIGR03830  74 RKKLGLSQREAAELLGGGVNAFSRYErgEVRPSKALDKLLRL 115
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 21-70 3.24e-05

Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. This family contains many example antitoxins from bacterial toxin-antitoxin systems. These antitoxins are likely to be DNA-binding domains.


Pssm-ID: 463728 [Multi-domain]  Cd Length: 64  Bit Score: 38.42  E-value: 3.24e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 582963866  21 RKANGLTQKDLSERLGVTQQTYSRLEANPASASIERLFKVFSILGVKISF 70
Cdd:pfam12844  8 REERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANW 57
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 20-61 1.53e-04

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 37.10  E-value: 1.53e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 582963866 20 FRKANGLTQKDLSERLGVTQQTYSRLEANPASASIE---RLFKVF 61
Cdd:COG3093  17 FLEPLGLSQTELAKALGVSRQRISEILNGKRAITADtalRLARAF 61
COG5606 COG5606
Predicted DNA-binding protein, XRE-type HTH domain [General function prediction only];
22-77 6.31e-04

Predicted DNA-binding protein, XRE-type HTH domain [General function prediction only];


Pssm-ID: 444337  Cd Length: 105  Bit Score: 35.63  E-value: 6.31e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 582963866  22 KANGLTQKDLSERLGVTQQTYSRL-EANPASASIERLFKVFSILG--VKISFSSATTSS 77
Cdd:COG5606   42 KERGLTQAEAAELLGITQPRVSDLlRGKISKFSLDKLVNMLARLGqdVEIVVRPARAAA 100
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
21-46 7.33e-04

DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 34.91  E-value: 7.33e-04
                        10        20
                ....*....|....*....|....*.
gi 582963866 21 RKANGLTQKDLSERLGVTQQTYSRLE 46
Cdd:COG2944  15 RERLGLSQAEFAALLGVSVSTVRRWE 40
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
25-69 1.21e-03

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 34.35  E-value: 1.21e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 582963866 25 GLTQKDLSERLGVTQQTYSRLEANPASA-SIERLFKVFSILGVKIS 69
Cdd:COG3655  14 GMTKKELAEATGISRATLSRLKNGKAKAvRLDTLEKICKALDCQPG 59
HTH_37 pfam13744
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain.
 12-68 3.77e-03

Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain.


Pssm-ID: 433449 [Multi-domain]  Cd Length: 80  Bit Score: 33.35  E-value: 3.77e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 582963866  12 QLRPLLIGFRKANGLTQKDLSERLGVTQQTYSRLE-ANPASASIERLFKVFSILGVKI 68
Cdd:pfam13744 18 QLARAIARLIEGRGLSQQEAAALLGIAQPKVSALLkGKLSRFSLDKLLDFLTALGQDV 75
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
17-63 4.25e-03

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 34.38  E-value: 4.25e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 582963866  17 LIGFRKANGLTQKDLSERLGVTQQTYSRLE---ANPASASIERLFKVFSI 63
Cdd:PRK09943  12 LSEIRQQQGLSQRRAAELSGLTHSAISTIEqdkVSPAISTLQKLLKVYGL 61
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 22-69 5.79e-03

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: 32.51  E-value: 5.79e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 582963866  22 KANGLTQKDLSERLGVTQQTYSRLEANPASA-SIERLFKVFSILGVKIS 69
Cdd:pfam13443  7 ADRGISKSDLARATGISRATLSRLRKGKPKRvSLDTLDKICDALGCQPG 55
mob_myst_A TIGR02612
mobile mystery protein A; Members of this protein family are found in mobization-related ...
 21-54 6.99e-03

mobile mystery protein A; Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381). [Unknown function, General]


Pssm-ID: 274231  Cd Length: 150  Bit Score: 33.63  E-value: 6.99e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 582963866   21 RKANGLTQKDLSERLGVTQQTYSRLEANPASASI 54
Cdd:TIGR02612  34 RKALGMSGAQLAGRLGVTPQRVEALEKSELSGTV 67
MarR_2 pfam12802
MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a ...
 9-45 9.58e-03

MarR family; The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.


Pssm-ID: 432797 [Multi-domain]  Cd Length: 60  Bit Score: 31.79  E-value: 9.58e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 582963866   9 TLNQLRpLLIGFRKANGLTQKDLSERLGVTQQTYSRL 45
Cdd:pfam12802  4 TPAQFR-VLLALARNPGLTVAELARRLGISKQTVSRL 39
 
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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