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Conserved domains on  [gi|505384107|ref|WP_015571209|]
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MULTISPECIES: helix-turn-helix transcriptional regulator [Enterobacter]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 10054599)

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
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 36-87 5.34e-11

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: 52.94  E-value: 5.34e-11
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 505384107 36 EMLAQWRNHAGLTRAQVAERMGVSAPTVSRMEANITRASLDTLTRYALVCGV 87
Cdd:cd00093   2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGV 53
 
Name Accession Description Interval E-value
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 36-87 5.34e-11

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: 52.94  E-value: 5.34e-11
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 505384107 36 EMLAQWRNHAGLTRAQVAERMGVSAPTVSRMEANITRASLDTLTRYALVCGV 87
Cdd:cd00093   2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGV 53
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
28-87 5.37e-11

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 53.46  E-value: 5.37e-11
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 505384107 28 EERKERLREMLAQWRNHAGLTRAQVAERMGVSAPTVSRMEANITRASLDTLTRYALVCGV 87
Cdd:COG1396   2 STLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGV 61
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
37-88 1.35e-10

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 51.75  E-value: 1.35e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 505384107   37 MLAQWRNHAGLTRAQVAERMGVSAPTVSRMEANITRASLDTLTRYALVCGVK 88
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVS 52
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 38-92 1.22e-09

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: 49.46  E-value: 1.22e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 505384107  38 LAQWRNHAGLTRAQVAERMGVSAPTVSRMEANITRASLDTLTRYALVCGVKHPQI 92
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 13-65 5.31e-05

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 39.90  E-value: 5.31e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 505384107  13 AELLSDSEVQASFDAEERKERLREMLAQWRNHA----------GLTRAQVAERMGVSAPTVSR 65
Cdd:PRK07408 176 GDLLPDPRYRSFQLAQEDRIRLQQALAQLEERTrevlefvflhDLTQKEAAERLGISPVTVSR 238
 
Name Accession Description Interval E-value
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 36-87 5.34e-11

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: 52.94  E-value: 5.34e-11
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 505384107 36 EMLAQWRNHAGLTRAQVAERMGVSAPTVSRMEANITRASLDTLTRYALVCGV 87
Cdd:cd00093   2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGV 53
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
28-87 5.37e-11

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 53.46  E-value: 5.37e-11
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 505384107 28 EERKERLREMLAQWRNHAGLTRAQVAERMGVSAPTVSRMEANITRASLDTLTRYALVCGV 87
Cdd:COG1396   2 STLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGV 61
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
37-88 1.35e-10

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 51.75  E-value: 1.35e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 505384107   37 MLAQWRNHAGLTRAQVAERMGVSAPTVSRMEANITRASLDTLTRYALVCGVK 88
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVS 52
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
31-87 6.05e-10

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 50.62  E-value: 6.05e-10
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 505384107 31 KERLREMLAQWRNHAGLTRAQVAERMGVSAPTVSRMEANITRASLDTLTRYALVCGV 87
Cdd:COG1476   2 KKKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGV 58
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 38-92 1.22e-09

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: 49.46  E-value: 1.22e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 505384107  38 LAQWRNHAGLTRAQVAERMGVSAPTVSRMEANITRASLDTLTRYALVCGVKHPQI 92
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 32-82 7.75e-09

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: 48.48  E-value: 7.75e-09
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 505384107 32 ERLREMLAQWRNHAGLTRAQVAERMGVSAPTVSRMEANITRASLDTLTRYA 82
Cdd:COG3620  16 DTLGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIA 66
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 33-87 5.60e-08

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: 45.21  E-value: 5.60e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 505384107  33 RLREMLAQWRNHAGLTRAQVAERMGVSAPTVSRMEA-NITRASLDTLTRYALVCGV 87
Cdd:pfam13560  1 ELGARLRRLRERAGLSQEALARRLGVSRSTLSRLETgRRGRPSPAVVERLARALGV 56
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 32-88 1.70e-06

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: 41.85  E-value: 1.70e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 505384107 32 ERLREMlaqwRNHAGLTRAQVAERMGVSAPTVSRMEANITRASLDTLTRYALVCGVK 88
Cdd:COG1813  15 ERIREA----REARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGIS 67
HTH_37 pfam13744
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain.
 26-82 1.43e-05

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: 39.52  E-value: 1.43e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 505384107  26 DAEERKERLREM--LAQWRNHAGLTRAQVAERMGVSAPTVSRME-ANITRASLDTLTRYA 82
Cdd:pfam13744  9 DAEELQAKAQLAraIARLIEGRGLSQQEAAALLGIAQPKVSALLkGKLSRFSLDKLLDFL 68
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 13-65 5.31e-05

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 39.90  E-value: 5.31e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 505384107  13 AELLSDSEVQASFDAEERKERLREMLAQWRNHA----------GLTRAQVAERMGVSAPTVSR 65
Cdd:PRK07408 176 GDLLPDPRYRSFQLAQEDRIRLQQALAQLEERTrevlefvflhDLTQKEAAERLGISPVTVSR 238
COG5606 COG5606
Predicted DNA-binding protein, XRE-type HTH domain [General function prediction only];
27-78 7.49e-05

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


Pssm-ID: 444337  Cd Length: 105  Bit Score: 38.33  E-value: 7.49e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 505384107  27 AEER--KERLREMLAQWRNHAGLTRAQVAERMGVSAPTVSR-MEANITRASLDTL 78
Cdd:COG5606   24 AEELklKAQLMAAIRKLIKERGLTQAEAAELLGITQPRVSDlLRGKISKFSLDKL 78
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 6-70 8.56e-05

DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA polymerase specialized sigma subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440804 [Multi-domain]  Cd Length: 236  Bit Score: 39.04  E-value: 8.56e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 505384107   6 IDWDELRAELLSDSEVQASFDAEERKERLREMLAQ----------WRNHAGLTRAQVAERMGVSAPTVSRMEANI 70
Cdd:COG1191  152 LEDGDDLLDLLESGDPEEELEHEELREALAEAIEQlpererlvlsLYYFEELTLKEIAEVLGVSESRVSRLHKKA 226
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
36-92 9.27e-05

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 37.22  E-value: 9.27e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 505384107 36 EMLAQWRNHAGLTRAQVAERMGVSAPTVSRMEANITRASLDTLTRYALVCgvKHPQI 92
Cdd:COG2944   9 EEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALKLLRLLE--KHPEL 63
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
31-80 1.84e-04

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 36.27  E-value: 1.84e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 505384107 31 KERLREMLAQwrnhAGLTRAQVAERMGVSAPTVSRMEAN-ITRASLDTLTR 80
Cdd:COG3655   3 YVKLDELLAE----RGMTKKELAEATGISRATLSRLKNGkAKAVRLDTLEK 49
COG3398 COG3398
Predicted transcriptional regulator, contains two HTH domains [Transcription];
20-83 1.99e-04

Predicted transcriptional regulator, contains two HTH domains [Transcription];


Pssm-ID: 442625 [Multi-domain]  Cd Length: 159  Bit Score: 37.94  E-value: 1.99e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 505384107  20 EVQASFDAEERK-------ERLREMLAQWRNHAGLTRAQVAERMGVSAPTVSR-----MEANITRASLDTL-TRYAL 83
Cdd:COG3398   78 PNSGTYSEEEKKilaylrrETPRRILLYLLENPGATNKELAEELGISRSTVSWhlkrlEEDGLVERERDGRnVRYYL 154
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 32-87 2.80e-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: 2.80e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 505384107 32 ERLREMLAQWRnhaGLTRAQVAERMGVSAPTVSRMEANITRASLDTLTRYALVCGV 87
Cdd:COG3093  11 EILREEFLEPL---GLSQTELAKALGVSRQRISEILNGKRAITADTALRLARAFGT 63
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 28-65 9.21e-04

Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a C-terminal DNA-binding domain (HTH_Hin) and a catalytic domain.


Pssm-ID: 259851 [Multi-domain]  Cd Length: 42  Bit Score: 33.84  E-value: 9.21e-04
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 505384107 28 EERKERLREMLAQwrnhaGLTRAQVAERMGVSAPTVSR 65
Cdd:cd00569   8 PEQIAEARRLLAA-----GESVAEIARELGVSRSTLYR 40
DeoR COG2390
DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];
44-66 1.28e-03

DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];


Pssm-ID: 441955 [Multi-domain]  Cd Length: 301  Bit Score: 35.88  E-value: 1.28e-03
                         10        20
                 ....*....|....*....|...
gi 505384107  44 HAGLTRAQVAERMGVSAPTVSRM 66
Cdd:COG2390    8 VEGLTQREIAERLGISRRTVSRL 30
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 29-69 1.61e-03

Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 441035 [Multi-domain]  Cd Length: 71  Bit Score: 34.01  E-value: 1.61e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 505384107 29 ERKERLREMLAQWRNHAGLTRAQVAERMGVSAPTVSRMEAN 69
Cdd:COG1426   1 EALETIGELLRQAREAKGLSLEDVAERTKISVSYLEAIEEG 41
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 32-87 3.68e-03

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: 33.03  E-value: 3.68e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 505384107  32 ERLREMlaqwRNHAGLTRAQVAERMGVSAPTVSRMEANITRASLDTLTRYALVCGV 87
Cdd:pfam12844  2 ERLRKA----REERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGV 53
PRK09775 PRK09775
type II toxin-antitoxin system HipA family toxin YjjJ;
38-85 4.88e-03

type II toxin-antitoxin system HipA family toxin YjjJ;


Pssm-ID: 236623 [Multi-domain]  Cd Length: 442  Bit Score: 34.55  E-value: 4.88e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 505384107  38 LAQWRNHAGLTRAQVAERMGVSAPTVSRMEANI---------TRAsldtlTRYALVC 85
Cdd:PRK09775   5 LTTLLLQGPLSAAELAARLGVSQATLSRLLAALgdqvvrfgkARA-----TRYALLR 56
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 33-78 7.27e-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: 32.13  E-value: 7.27e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 505384107  33 RLREMLAQwrnhAGLTRAQVAERMGVSAPTVSRMEAN-ITRASLDTL 78
Cdd:pfam13443  1 KLRKLMAD----RGISKSDLARATGISRATLSRLRKGkPKRVSLDTL 43
 
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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