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Conserved domains on  [gi|489139486|ref|WP_003049262|]
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helix-turn-helix domain-containing protein [Thermus aquaticus]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 11443570)

helix-turn-helix domain-containing protein such as an XRE (Xenobiotic Response Element) family transcriptional regulator

Gene Ontology:  GO:0003677
PubMed:  37972151

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
14-77 1.82e-12

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 60.78  E-value: 1.82e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489139486  14 ARLVERRKALGLTQEGLARLAGFSTSLMAKIERGAvdlRSLSAQHVVGLAKALGLPLNALLDED 77
Cdd:COG1396   10 ERLRELRKARGLTQEELAERLGVSRSTISRIERGR---RNPSLETLLKLAKALGVSLDELLGGA 70
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
14-77 1.82e-12

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 60.78  E-value: 1.82e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489139486  14 ARLVERRKALGLTQEGLARLAGFSTSLMAKIERGAvdlRSLSAQHVVGLAKALGLPLNALLDED 77
Cdd:COG1396   10 ERLRELRKARGLTQEELAERLGVSRSTISRIERGR---RNPSLETLLKLAKALGVSLDELLGGA 70
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 15-73 3.00e-09

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: 51.40  E-value: 3.00e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 489139486  15 RLVERRKALGLTQEGLARLAGFSTSLMAKIERGavdLRSLSAQHVVGLAKALGLPLNAL 73
Cdd:cd00093    3 RLKELRKEKGLTQEELAEKLGVSRSTISRIENG---KRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
15-73 4.62e-09

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 50.59  E-value: 4.62e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 489139486    15 RLVERRKALGLTQEGLARLAGFSTSLMAKIERGavdLRSLSAQHVVGLAKALGLPLNAL 73
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENG---KRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 18-73 2.42e-07

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: 45.99  E-value: 2.42e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 489139486   18 ERRKALGLTQEGLARLAGFSTSLMAKIERGavdLRSLSAQHVVGLAKALGLPLNAL 73
Cdd:pfam01381   3 ELREELGLSQEELAEKLGVSRSTISKIENG---KREPSLETLKKLAEALGVSLDEL 55
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 16-70 4.46e-06

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: 42.65  E-value: 4.46e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 489139486   16 LVERRKALGLTQEGLARLAGFSTSLMAKIERGAvdlRSLSAQHVVGLAKALGLPL 70
Cdd:TIGR03070   7 VRARRKALGLTQADLADLAGVGLRFIRDLENGK---PTVRLDKVLRVLDALGLEL 58
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
15-98 1.77e-04

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 40.93  E-value: 1.77e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489139486  15 RLVERRKALGLTQEGLARLAGFSTSLMAKIERGAVdlrSLSAQHVVGLAKALGLPLNALLDEDLPGGEVAkplllpVYRA 94
Cdd:PRK09943  11 RLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKV---SPAISTLQKLLKVYGLSLSEFFSEPEKPDEPQ------VVIN 81


                 ....
gi 489139486  95 PEDL 98
Cdd:PRK09943  82 QDDL 85
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
14-77 1.82e-12

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 60.78  E-value: 1.82e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489139486  14 ARLVERRKALGLTQEGLARLAGFSTSLMAKIERGAvdlRSLSAQHVVGLAKALGLPLNALLDED 77
Cdd:COG1396   10 ERLRELRKARGLTQEELAERLGVSRSTISRIERGR---RNPSLETLLKLAKALGVSLDELLGGA 70
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
15-77 5.83e-10

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 53.70  E-value: 5.83e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489139486  15 RLVERRKALGLTQEGLARLAGFSTSLMAKIERGAvdlRSLSAQHVVGLAKALGLPLNALLDED 77
Cdd:COG1476    8 RLKELRKERGLTQEELAELLGVSRQTISAIENGK---YNPSLELALKIARALGVSLEELFSLE 67
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 15-73 3.00e-09

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: 51.40  E-value: 3.00e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 489139486  15 RLVERRKALGLTQEGLARLAGFSTSLMAKIERGavdLRSLSAQHVVGLAKALGLPLNAL 73
Cdd:cd00093    3 RLKELRKEKGLTQEELAEKLGVSRSTISRIENG---KRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
15-73 4.62e-09

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 50.59  E-value: 4.62e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 489139486    15 RLVERRKALGLTQEGLARLAGFSTSLMAKIERGavdLRSLSAQHVVGLAKALGLPLNAL 73
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENG---KRKPSLETLKKLAKALGVSLDEL 56
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 1-70 8.16e-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: 47.63  E-value: 8.16e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489139486   1 MPRTPRNPLPPRVA-RLVERRKALGLTQEGLARLAGFSTSLMAKIERGavdLRSLSAQHVVGLAKALGLPL 70
Cdd:COG1813    1 MAKESTGELVEDYGeRIREAREARGLSQEELAEKLGVSESTIRRIERG---EATPSLDTLRKLEKALGISL 68
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 18-73 2.42e-07

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: 45.99  E-value: 2.42e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 489139486   18 ERRKALGLTQEGLARLAGFSTSLMAKIERGavdLRSLSAQHVVGLAKALGLPLNAL 73
Cdd:pfam01381   3 ELREELGLSQEELAEKLGVSRSTISKIENG---KREPSLETLKKLAEALGVSLDEL 55
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 16-70 4.46e-06

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: 42.65  E-value: 4.46e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 489139486   16 LVERRKALGLTQEGLARLAGFSTSLMAKIERGAvdlRSLSAQHVVGLAKALGLPL 70
Cdd:TIGR03070   7 VRARRKALGLTQADLADLAGVGLRFIRDLENGK---PTVRLDKVLRVLDALGLEL 58
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 15-74 9.18e-06

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: 41.89  E-value: 9.18e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 489139486   15 RLVERRKALGLTQEGLARLAGFSTSLMAKIERGavdLRSLSAQHVVGLAKALGLPLNALL 74
Cdd:pfam12844   3 RLRKAREERGLTQEELAERLGISRSQLSAIENG---KSVPPAETLYKIAELLGVPANWLL 59
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 14-69 1.02e-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: 41.74  E-value: 1.02e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 489139486   14 ARLVERRKALGLTQEGLARLAGFSTSLMAKIERGAVDLRSLSAqhVVGLAKALGLP 69
Cdd:pfam13560   4 ARLRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGRPSPAV--VERLARALGVD 57
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 16-77 1.55e-05

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: 42.31  E-value: 1.55e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489139486  16 LVERRKALGLTQEGLARLAGFSTSLMAKIERGAVDLRsLSAqhVVGLAKALGLPLNALLDED 77
Cdd:COG3620   22 LRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPT-VST--LEKIAEALGKELSAVLVVD 80
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 14-74 1.26e-04

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: 39.02  E-value: 1.26e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489139486  14 ARLVERRKALGLTQEGLARLAGFSTSLMAKIERGAVDlRSLSAQHVVG----LAKALGLPLNALL 74
Cdd:COG1426    8 ELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGDFD-ALPGPVYVRGflrsYARALGLDPEELL 71
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
15-98 1.77e-04

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 40.93  E-value: 1.77e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489139486  15 RLVERRKALGLTQEGLARLAGFSTSLMAKIERGAVdlrSLSAQHVVGLAKALGLPLNALLDEDLPGGEVAkplllpVYRA 94
Cdd:PRK09943  11 RLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKV---SPAISTLQKLLKVYGLSLSEFFSEPEKPDEPQ------VVIN 81


                 ....
gi 489139486  95 PEDL 98
Cdd:PRK09943  82 QDDL 85
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 14-111 4.14e-04

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 39.07  E-value: 4.14e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489139486  14 ARLVERRKALGLTQEGLARLAGFSTSLMAKIERGAVDLRslsAQHVVGLAKALGLPLNALL--DEDLPGGEVAkPLLLPV 91
Cdd:PRK09706   8 QRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPT---GKNLFALAKALQCSPTWLLfgDEDKQPTPPV-PLNQPV 83

                         90       100
                 ....*....|....*....|
gi 489139486  92 YRAPEDlaREDVERFAITPE 111
Cdd:PRK09706  84 ELSEDQ--KELLELFDALPE 101
PRK13355 PRK13355
bifunctional HTH-domain containing protein/aminotransferase; Provisional
 14-79 5.97e-03

bifunctional HTH-domain containing protein/aminotransferase; Provisional


Pssm-ID: 237361 [Multi-domain]  Cd Length: 517  Bit Score: 37.02  E-value: 5.97e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489139486  14 ARLVERRKALGLTQEGLARLAG-----FSTSLMAKIERGAVDLRSlSAQHVvgLAKALGLPLNALLDEDLP 79
Cdd:PRK13355   6 ERLKQAMKARGLKQEDLVHAAEargvkLGKSHISQYVSGKTGPRR-DVLPF--LAAILGVSEDWLLGGESP 73
 
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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