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Conserved domains on  [gi|445944090|ref|WP_000021945|]
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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];
1-78 2.53e-21

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 81.97  E-value: 2.53e-21
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 445944090   1 MSIGEQLKKLRESKEFSQEDVAKKIGVTRQAVYKWENDKSYPDIDNLILLSEMYNVTLDELIKGNQSFKEKIHIDEEE 78
Cdd:COG1396    6 KALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPEALLSEEE 83
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-78 2.53e-21

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 81.97  E-value: 2.53e-21
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 445944090   1 MSIGEQLKKLRESKEFSQEDVAKKIGVTRQAVYKWENDKSYPDIDNLILLSEMYNVTLDELIKGNQSFKEKIHIDEEE 78
Cdd:COG1396    6 KALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPEALLSEEE 83
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 4-61 1.70e-17

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: 71.43  E-value: 1.70e-17
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 445944090   4 GEQLKKLRESKEFSQEDVAKKIGVTRQAVYKWENDKSYPDIDNLILLSEMYNVTLDEL 61
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 7-61 2.21e-16

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: 68.34  E-value: 2.21e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 445944090    7 LKKLRESKEFSQEDVAKKIGVTRQAVYKWENDKSYPDIDNLILLSEMYNVTLDEL 61
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
7-61 4.39e-16

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 67.54  E-value: 4.39e-16
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 445944090     7 LKKLRESKEFSQEDVAKKIGVTRQAVYKWENDKSYPDIDNLILLSEMYNVTLDEL 61
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
PHA01976 PHA01976
helix-turn-helix protein
 1-64 7.73e-09

helix-turn-helix protein


Pssm-ID: 177330 [Multi-domain]  Cd Length: 67  Bit Score: 49.18  E-value: 7.73e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 445944090   1 MSIGEQLKKLRESKEFSQEDVAKKIGVTRQAVYKWENDKSYPDIDNLILLSEMYNVTLDELIKG 64
Cdd:PHA01976   1 MSFAIQLIKARNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTLDWLCGR 64
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 3-48 4.47e-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: 38.00  E-value: 4.47e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 445944090    3 IGEQLKKLRESKEFSQEDVAKKIGVTRQAVYKWENDKSYPD--IDNLI 48
Cdd:TIGR03830  66 TGPEIRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSkaLDKLL 113
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-78 2.53e-21

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 81.97  E-value: 2.53e-21
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 445944090   1 MSIGEQLKKLRESKEFSQEDVAKKIGVTRQAVYKWENDKSYPDIDNLILLSEMYNVTLDELIKGNQSFKEKIHIDEEE 78
Cdd:COG1396    6 KALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPEALLSEEE 83
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-66 3.33e-19

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 76.04  E-value: 3.33e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 445944090   1 MSIGEQLKKLRESKEFSQEDVAKKIGVTRQAVYKWENDKSYPDIDNLILLSEMYNVTLDELIKGNQ 66
Cdd:COG1476    3 KKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 4-61 1.70e-17

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: 71.43  E-value: 1.70e-17
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 445944090   4 GEQLKKLRESKEFSQEDVAKKIGVTRQAVYKWENDKSYPDIDNLILLSEMYNVTLDEL 61
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 7-61 2.21e-16

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: 68.34  E-value: 2.21e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 445944090    7 LKKLRESKEFSQEDVAKKIGVTRQAVYKWENDKSYPDIDNLILLSEMYNVTLDEL 61
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
7-61 4.39e-16

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 67.54  E-value: 4.39e-16
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 445944090     7 LKKLRESKEFSQEDVAKKIGVTRQAVYKWENDKSYPDIDNLILLSEMYNVTLDEL 61
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 3-60 8.04e-13

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: 59.57  E-value: 8.04e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 445944090   3 IGEQLKKLRESKEFSQEDVAKKIGVTRQAVYKWENDKSYPDIDNLILLSEMYNVTLDE 60
Cdd:COG1813   13 YGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLAE 70
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 1-62 1.33e-10

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: 54.64  E-value: 1.33e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 445944090   1 MSIGEQLKKLRESKEFSQEDVAKKIGVTRQAVYKWENDKSYPDIDNLILLSEMYNVTLDELI 62
Cdd:COG3620   16 DTLGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVL 77
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 4-64 2.54e-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: 53.06  E-value: 2.54e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 445944090    4 GEQLKKLRESKEFSQEDVAKKIGVTRQAVYKWENDKSYPDIDNLILLSEMYNVTLDELIKG 64
Cdd:pfam12844   1 GERLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLLQG 61
PHA01976 PHA01976
helix-turn-helix protein
 1-64 7.73e-09

helix-turn-helix protein


Pssm-ID: 177330 [Multi-domain]  Cd Length: 67  Bit Score: 49.18  E-value: 7.73e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 445944090   1 MSIGEQLKKLRESKEFSQEDVAKKIGVTRQAVYKWENDKSYPDIDNLILLSEMYNVTLDELIKG 64
Cdd:PHA01976   1 MSFAIQLIKARNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTLDWLCGR 64
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
4-55 3.04e-08

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 47.62  E-value: 3.04e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 445944090   4 GEQLKKLRESKEFSQEDVAKKIGVTRQAVYKWENDKSYPDIDNLILLSEMYN 55
Cdd:COG2944    8 PEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALKLLRLLEK 59
PRK04140 PRK04140
transcriptional regulator;
4-84 7.33e-07

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 47.16  E-value: 7.33e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445944090   4 GEQLKKLRESKEFSQEDVAKKIGVTRQAVYKWENDKSYPDIDNLILLSEMYNVTLDE---LIKGNQSfKEKIHIDEEEAD 80
Cdd:PRK04140 128 GDVLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDVPLTKpidILEKVRD-DEVTPEDPEEDP 206


                 ....
gi 445944090  81 FEKE 84
Cdd:PRK04140 207 FEKE 210
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 3-61 8.57e-07

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: 43.67  E-value: 8.57e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 445944090    3 IGEQLKKLRESKEFSQEDVAKKIGVTRQAVYKWENDK-SYPDIDNLILLSEMYNVTLDEL 61
Cdd:pfam13560   2 LGARLRRLRERAGLSQEALARRLGVSRSTLSRLETGRrGRPSPAVVERLARALGVDGAER 61
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 1-39 1.45e-06

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: 43.25  E-value: 1.45e-06
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 445944090   1 MSIGEQLKKLRESKEFSQEDVAKKIGVTRQAVYKWENDK 39
Cdd:COG1426    4 ETIGELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGD 42
COG1395 COG1395
Predicted transcriptional regulator [Transcription];
4-86 9.75e-06

Predicted transcriptional regulator [Transcription];


Pssm-ID: 441005 [Multi-domain]  Cd Length: 313  Bit Score: 43.67  E-value: 9.75e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445944090   4 GEQLKKLRESKEFSQEDVAKKIGVTRQAVYKWENDKSYPDIDNLILLSEMYNvtlDELIKGNQSFKEKIHIDEEEADFEK 83
Cdd:COG1395  129 GEKLRELREERGLSLGELASELGVSRRTISKYERGEMDASIEVALKLEEILG---EPIVKPIDILEGAEDLEEAEPTPED 205


                 ...
gi 445944090  84 ENE 86
Cdd:COG1395  206 PEE 208
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 7-63 3.46e-05

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: 39.45  E-value: 3.46e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 445944090    7 LKKLRESKEFSQEDVAKKIGVTRQAVYKWENDKS-YPDIDNLILLSEMYNVTLDELIK 63
Cdd:pfam13443   2 LRKLMADRGISKSDLARATGISRATLSRLRKGKPkRVSLDTLDKICDALGCQPGDLLE 59
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 2-52 4.70e-05

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 40.61  E-value: 4.70e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 445944090   2 SIGEQLKKLRESKEFSQEDVAKKIGVTRQAVYKWENDKSYPDIDNLILLSE 52
Cdd:PRK09706   5 TLGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAK 55
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
4-78 4.17e-04

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 38.62  E-value: 4.17e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 445944090   4 GEQLKKLRESKEFSQEDVAKKIGVTRQAVYKWENDKSYPDIDNLILLSEMYNVTLDELIKGNQSFKE-KIHIDEEE 78
Cdd:PRK09943   9 GKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFFSEPEKPDEpQVVINQDD 84
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 3-48 4.47e-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: 38.00  E-value: 4.47e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 445944090    3 IGEQLKKLRESKEFSQEDVAKKIGVTRQAVYKWENDKSYPD--IDNLI 48
Cdd:TIGR03830  66 TGPEIRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSkaLDKLL 113
 
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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