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Conserved domains on  [gi|446427765|ref|WP_000505620|]
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MULTISPECIES: helix-turn-helix domain-containing protein [Bacillus]

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];
1-73 6.17e-20

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 81.58  E-value: 6.17e-20
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446427765   1 MGFGEKLFKLRKEKGLSQEALAEKLNTTRQAVSKWENGQGFPETEKLIMIGNVFEVSLDYLLKETAEQSNENV 73
Cdd:COG1396    6 KALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPEAL 78
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-73 6.17e-20

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 81.58  E-value: 6.17e-20
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446427765   1 MGFGEKLFKLRKEKGLSQEALAEKLNTTRQAVSKWENGQGFPETEKLIMIGNVFEVSLDYLLKETAEQSNENV 73
Cdd:COG1396    6 KALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPEAL 78
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 4-61 9.25e-15

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: 66.81  E-value: 9.25e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446427765   4 GEKLFKLRKEKGLSQEALAEKLNTTRQAVSKWENGQGFPETEKLIMIGNVFEVSLDYL 61
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
6-61 1.97e-13

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 63.31  E-value: 1.97e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 446427765     6 KLFKLRKEKGLSQEALAEKLNTTRQAVSKWENGQGFPETEKLIMIGNVFEVSLDYL 61
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 7-61 2.26e-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: 60.25  E-value: 2.26e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 446427765    7 LFKLRKEKGLSQEALAEKLNTTRQAVSKWENGQGFPETEKLIMIGNVFEVSLDYL 61
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
PRK13355 PRK13355
bifunctional HTH-domain containing protein/aminotransferase; Provisional
 3-71 1.92e-06

bifunctional HTH-domain containing protein/aminotransferase; Provisional


Pssm-ID: 237361 [Multi-domain]  Cd Length: 517  Bit Score: 48.58  E-value: 1.92e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446427765   3 FGEKLFKLRKEKGLSQEAL---AEKLNT--TRQAVSKWENGQGFPETEKLIMIGNVFEVSLDYLLKETAEQSNE 71
Cdd:PRK13355   4 FAERLKQAMKARGLKQEDLvhaAEARGVklGKSHISQYVSGKTGPRRDVLPFLAAILGVSEDWLLGGESPADQE 77
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 9-50 3.26e-04

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: 3.26e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 446427765    9 KLRKEKGLSQEALAEKLNTTRQAVSKWENGQGFPE--TEKLIMI 50
Cdd:TIGR03830  72 RIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSkaLDKLLRL 115
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-73 6.17e-20

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 81.58  E-value: 6.17e-20
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446427765   1 MGFGEKLFKLRKEKGLSQEALAEKLNTTRQAVSKWENGQGFPETEKLIMIGNVFEVSLDYLLKETAEQSNENV 73
Cdd:COG1396    6 KALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPEAL 78
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-65 4.57e-16

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 70.65  E-value: 4.57e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446427765   1 MGFGEKLFKLRKEKGLSQEALAEKLNTTRQAVSKWENGQGFPETEKLIMIGNVFEVSLDYLLKET 65
Cdd:COG1476    3 KKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLE 67
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 4-61 9.25e-15

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: 66.81  E-value: 9.25e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446427765   4 GEKLFKLRKEKGLSQEALAEKLNTTRQAVSKWENGQGFPETEKLIMIGNVFEVSLDYL 61
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
6-61 1.97e-13

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 63.31  E-value: 1.97e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 446427765     6 KLFKLRKEKGLSQEALAEKLNTTRQAVSKWENGQGFPETEKLIMIGNVFEVSLDYL 61
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 3-60 1.22e-12

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: 61.49  E-value: 1.22e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446427765   3 FGEKLFKLRKEKGLSQEALAEKLNTTRQAVSKWENGQGFPETEKLIMIGNVFEVSLDY 60
Cdd:COG1813   13 YGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLAE 70
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 7-61 2.26e-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: 60.25  E-value: 2.26e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 446427765    7 LFKLRKEKGLSQEALAEKLNTTRQAVSKWENGQGFPETEKLIMIGNVFEVSLDYL 61
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 4-67 2.56e-10

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: 54.99  E-value: 2.56e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446427765    4 GEKLFKLRKEKGLSQEALAEKLNTTRQAVSKWENGQGFPETEKLIMIGNVFEVSLDYLLKETAE 67
Cdd:pfam12844   1 GERLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLLQGEGE 64
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
4-42 2.07e-07

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 46.85  E-value: 2.07e-07
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 446427765   4 GEKLFKLRKEKGLSQEALAEKLNTTRQAVSKWENGQGFP 42
Cdd:COG2944    8 PEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKP 46
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 3-59 1.49e-06

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: 44.44  E-value: 1.49e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 446427765    3 FGEKLFKLRKEKGLSQEALAEKLNTTRQAVSKWENG-QGFPETEKLIMIGNVFEVSLD 59
Cdd:pfam13560   2 LGARLRRLRERAGLSQEALARRLGVSRSTLSRLETGrRGRPSPAVVERLARALGVDGA 59
PRK13355 PRK13355
bifunctional HTH-domain containing protein/aminotransferase; Provisional
 3-71 1.92e-06

bifunctional HTH-domain containing protein/aminotransferase; Provisional


Pssm-ID: 237361 [Multi-domain]  Cd Length: 517  Bit Score: 48.58  E-value: 1.92e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446427765   3 FGEKLFKLRKEKGLSQEAL---AEKLNT--TRQAVSKWENGQGFPETEKLIMIGNVFEVSLDYLLKETAEQSNE 71
Cdd:PRK13355   4 FAERLKQAMKARGLKQEDLvhaAEARGVklGKSHISQYVSGKTGPRRDVLPFLAAILGVSEDWLLGGESPADQE 77
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 3-62 2.81e-06

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: 44.63  E-value: 2.81e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446427765   3 FGEKLFKLRKEKGLSQEALAEKLNTTRQAVSKWENGQGFPETEKLIMIGNVFEVSLDYLL 62
Cdd:COG3620   18 LGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVL 77
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 3-62 5.80e-06

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 44.84  E-value: 5.80e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446427765   3 FGEKLFKLRKEKGLSQEALAEKLNTTRQAVSKWENGQGFPETEKLIMIGNVFEVSLDYLL 62
Cdd:PRK09706   6 LGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCSPTWLL 65
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 1-39 2.13e-05

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: 41.71  E-value: 2.13e-05
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 446427765   1 MGFGEKLFKLRKEKGLSQEALAEKLNTTRQAVSKWENGQ 39
Cdd:COG1426    4 ETIGELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGD 42
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 12-62 6.19e-05

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 40.56  E-value: 6.19e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 446427765  12 KEKGLSQEALAEKLNTTRQAVSKWENGQGFPETEKLIMIGNVFEVSLDYLL 62
Cdd:COG3093   19 EPLGLSQTELAKALGVSRQRISEILNGKRAITADTALRLARAFGTSAEFWL 69
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
4-73 6.93e-05

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 42.47  E-value: 6.93e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446427765   4 GEKLFKLRKEKGLSQEALAEKLNTTRQAVSKWENGQGFPETEKLIMIGNVFEVSLDYLLKETAEQSNENV 73
Cdd:PRK09943   9 GKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFFSEPEKPDEPQV 78
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 9-50 3.26e-04

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: 3.26e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 446427765    9 KLRKEKGLSQEALAEKLNTTRQAVSKWENGQGFPE--TEKLIMI 50
Cdd:TIGR03830  72 RIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSkaLDKLLRL 115
YdaS COG4197
DNA-binding transcriptional regulator YdaS, prophage-encoded, Cro superfamily [Transcription];
17-40 4.38e-04

DNA-binding transcriptional regulator YdaS, prophage-encoded, Cro superfamily [Transcription];


Pssm-ID: 443351  Cd Length: 68  Bit Score: 37.97  E-value: 4.38e-04
                         10        20
                 ....*....|....*....|....
gi 446427765  17 SQEALAEKLNTTRQAVSKWENGQG 40
Cdd:COG4197   10 SQSALARALGVSQQAVSQWLNGKR 33
COG1395 COG1395
Predicted transcriptional regulator [Transcription];
4-58 4.45e-04

Predicted transcriptional regulator [Transcription];


Pssm-ID: 441005 [Multi-domain]  Cd Length: 313  Bit Score: 40.98  E-value: 4.45e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 446427765   4 GEKLFKLRKEKGLSQEALAEKLNTTRQAVSKWENGQGFPETEKLIMIGNVFEVSL 58
Cdd:COG1395  129 GEKLRELREERGLSLGELASELGVSRRTISKYERGEMDASIEVALKLEEILGEPI 183
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 3-50 6.61e-04

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: 36.87  E-value: 6.61e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 446427765    3 FGEKLFKLRKEKGLSQEALAEKLNTTRQAVSKWENGQGFPETEKLIMI 50
Cdd:TIGR03070   3 IGILVRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRV 50
PHA01976 PHA01976
helix-turn-helix protein
 1-67 7.19e-04

helix-turn-helix protein


Pssm-ID: 177330 [Multi-domain]  Cd Length: 67  Bit Score: 37.24  E-value: 7.19e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446427765   1 MGFGEKLFKLRKEKGLSQEALAEKLNTTRQAVSKWENGQGFPETEKLIMIGNVFEVSLDYLLKETAE 67
Cdd:PHA01976   1 MSFAIQLIKARNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTLDWLCGRCGE 67
PRK04140 PRK04140
transcriptional regulator;
4-76 1.40e-03

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 39.46  E-value: 1.40e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446427765   4 GEKLFKLRKEKGLSQEALAEKLNTTRQAVSKWENGQGFPETEKLIMIGNVFEVSL-------DYLLKETAEQSNENVDGY 76
Cdd:PRK04140 128 GDVLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDVPLtkpidilEKVRDDEVTPEDPEEDPF 207
YdaS_antitoxin pfam15943
Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT; YdaS_antitoxin is a family ...
 17-40 5.75e-03

Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT; YdaS_antitoxin is a family of putative bacterial antitoxins, neutralising the toxin YdaT, family pfam06254.


Pssm-ID: 435033  Cd Length: 65  Bit Score: 34.63  E-value: 5.75e-03
                          10        20
                  ....*....|....*....|....
gi 446427765   17 SQEALAEKLNTTRQAVSKWENGQG 40
Cdd:pfam15943  10 GQKALAEALGVTQQAVSQWLHGKK 33
 
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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