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Conserved domains on  [gi|545062094|ref|WP_021435039|]
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MULTISPECIES: helix-turn-helix domain-containing protein [Bacillota]

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];
3-67 3.35e-16

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 68.10  E-value: 3.35e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 545062094   3 MNNISPQ-SKRIRELRIELQLSQEDFAERLKLKRNTISLIENGKRNASNRTLKDICDAWSVSYDWL 67
Cdd:COG1396    1 MSTLKKAlGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDEL 66
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
3-67 3.35e-16

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 68.10  E-value: 3.35e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 545062094   3 MNNISPQ-SKRIRELRIELQLSQEDFAERLKLKRNTISLIENGKRNASNRTLKDICDAWSVSYDWL 67
Cdd:COG1396    1 MSTLKKAlGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDEL 66
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
12-67 8.70e-13

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 58.68  E-value: 8.70e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 545062094    12 RIRELRIELQLSQEDFAERLKLKRNTISLIENGKRNASNRTLKDICDAWSVSYDWL 67
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
10-67 2.02e-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: 57.56  E-value: 2.02e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 545062094  10 SKRIRELRIELQLSQEDFAERLKLKRNTISLIENGKRNASNRTLKDICDAWSVSYDWL 67
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
11-72 6.35e-11

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: 53.83  E-value: 6.35e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 545062094   11 KRIRELRIELQLSQEDFAERLKLKRNTISLIENGKRNASNRTLKDICDAWSVSYDWLANGIG 72
Cdd:pfam12844   2 ERLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLLQGEG 63
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
13-59 7.91e-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: 40.72  E-value: 7.91e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 545062094   13 IRELRIELQLSQEDFAERLKLKRNTISLIENGKRNASNRTLKDICDA 59
Cdd:TIGR03070   7 VRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDA 53
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
1-63 1.40e-05

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 42.47  E-value: 1.40e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 545062094   1 MDMNNISPqSKRIRELRIELQLSQEDFAERLKLKRNTISLIENGKRNASNRTLKDICDAWSVS 63
Cdd:PRK09943   1 MSDEGLAP-GKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLS 62
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
3-67 3.35e-16

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 68.10  E-value: 3.35e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 545062094   3 MNNISPQ-SKRIRELRIELQLSQEDFAERLKLKRNTISLIENGKRNASNRTLKDICDAWSVSYDWL 67
Cdd:COG1396    1 MSTLKKAlGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDEL 66
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
10-67 1.45e-13

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 61.02  E-value: 1.45e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 545062094  10 SKRIRELRIELQLSQEDFAERLKLKRNTISLIENGKRNASNRTLKDICDAWSVSYDWL 67
Cdd:COG1476    6 GNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEEL 63
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
12-67 8.70e-13

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 58.68  E-value: 8.70e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 545062094    12 RIRELRIELQLSQEDFAERLKLKRNTISLIENGKRNASNRTLKDICDAWSVSYDWL 67
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
10-67 2.02e-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: 57.56  E-value: 2.02e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 545062094  10 SKRIRELRIELQLSQEDFAERLKLKRNTISLIENGKRNASNRTLKDICDAWSVSYDWL 67
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
11-72 6.35e-11

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: 53.83  E-value: 6.35e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 545062094   11 KRIRELRIELQLSQEDFAERLKLKRNTISLIENGKRNASNRTLKDICDAWSVSYDWLANGIG 72
Cdd:pfam12844   2 ERLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLLQGEG 63
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
13-67 6.56e-11

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: 53.70  E-value: 6.56e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 545062094   13 IRELRIELQLSQEDFAERLKLKRNTISLIENGKRNASNRTLKDICDAWSVSYDWL 67
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
11-66 7.30e-11

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: 54.17  E-value: 7.30e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 545062094  11 KRIRELRIELQLSQEDFAERLKLKRNTISLIENGKRNASNRTLKDICDAWSVSYDW 66
Cdd:COG1813   15 ERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLAE 70
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
12-59 5.10e-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: 46.37  E-value: 5.10e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 545062094   12 RIRELRIELQLSQEDFAERLKLKRNTISLIENGKRN-ASNRTLKDICDA 59
Cdd:pfam13560   5 RLRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGrPSPAVVERLARA 53
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
3-54 1.36e-07

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 45.31  E-value: 1.36e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 545062094   3 MNNISPQSKRIRELRIELQLSQEDFAERLKLKRNTISLIENGKRNASNRTLK 54
Cdd:COG2944    1 MTKKPLTPEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALK 52
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
13-67 2.09e-07

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: 45.78  E-value: 2.09e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 545062094  13 IRELRIELQLSQEDFAERLKLKRNTISLIENGKRNASNRTLKDICDAWSVSYDWL 67
Cdd:COG3620   22 LRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAV 76
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
11-48 4.03e-07

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: 44.41  E-value: 4.03e-07
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 545062094  11 KRIRELRIELQLSQEDFAERLKLKRNTISLIENGKRNA 48
Cdd:COG1426    8 ELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGDFDA 45
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
13-59 7.91e-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: 40.72  E-value: 7.91e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 545062094   13 IRELRIELQLSQEDFAERLKLKRNTISLIENGKRNASNRTLKDICDA 59
Cdd:TIGR03070   7 VRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDA 53
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
1-63 1.40e-05

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 42.47  E-value: 1.40e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 545062094   1 MDMNNISPqSKRIRELRIELQLSQEDFAERLKLKRNTISLIENGKRNASNRTLKDICDAWSVS 63
Cdd:PRK09943   1 MSDEGLAP-GKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLS 62
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
1-47 8.50e-05

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 38.64  E-value: 8.50e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 545062094   1 MDMNNISPQSKRIRELRIE-LQLSQEDFAERLKLKRNTISLIENGKRN 47
Cdd:COG3093    1 MNKRNPIHPGEILREEFLEpLGLSQTELAKALGVSRQRISEILNGKRA 48
PRK10856 PRK10856
cytoskeleton protein RodZ;
12-49 1.21e-03

cytoskeleton protein RodZ;


Pssm-ID: 236776 [Multi-domain]  Cd Length: 331  Bit Score: 37.31  E-value: 1.21e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 545062094  12 RIRELRIELQLSQEDFAERLKLKRNTISLIENGKRNAS 49
Cdd:PRK10856  18 RLRQAREQLGLTQQAVAERLCLKVSTVRDIEEDKAPAD 55
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
11-59 2.38e-03

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 34.35  E-value: 2.38e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 545062094  11 KRIRELRIELQLSQEDFAERLKLKRNTISLIENGK-RNASNRTLKDICDA 59
Cdd:COG3655    4 VKLDELLAERGMTKKELAEATGISRATLSRLKNGKaKAVRLDTLEKICKA 53
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
12-59 2.94e-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: 34.05  E-value: 2.94e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 545062094   12 RIRELRIELQLSQEDFAERLKLKRNTISLIENGK-RNASNRTLKDICDA 59
Cdd:pfam13443   1 KLRKLMADRGISKSDLARATGISRATLSRLRKGKpKRVSLDTLDKICDA 49
HTH_25 pfam13413
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
12-45 3.34e-03

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


Pssm-ID: 433187 [Multi-domain]  Cd Length: 62  Bit Score: 33.62  E-value: 3.34e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 545062094   12 RIRELRIELQLSQEDFAERLKLKRNTISLIENGK 45
Cdd:pfam13413   1 RLRAAREARGLSLEDVAERTKIRPRYLEALEEDD 34
PRK13355 PRK13355
bifunctional HTH-domain containing protein/aminotransferase; Provisional
6-70 4.96e-03

bifunctional HTH-domain containing protein/aminotransferase; Provisional


Pssm-ID: 237361 [Multi-domain]  Cd Length: 517  Bit Score: 35.48  E-value: 4.96e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 545062094   6 ISPQSKRIRELRIELQLSQEDFAERL-----KLKRNTISLIENGKRNASNRTLKDICDAWSVSYDWLANG 70
Cdd:PRK13355   1 KTTFAERLKQAMKARGLKQEDLVHAAeargvKLGKSHISQYVSGKTGPRRDVLPFLAAILGVSEDWLLGG 70
 
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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