NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|505337243|ref|WP_015524345|]
View 

MULTISPECIES: helix-turn-helix domain-containing protein [Clostridia]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
4-65 1.28e-17

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 69.26  E-value: 1.28e-17
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 505337243  4 QRIQDLRTDADLSQRELSEILHISQRSYSHYETGSRNIPIEMLIRLANYYDTSIDYLVGRTD 65
Cdd:COG1396  10 ERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGAD 71
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
4-65 1.28e-17

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 69.26  E-value: 1.28e-17
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 505337243  4 QRIQDLRTDADLSQRELSEILHISQRSYSHYETGSRNIPIEMLIRLANYYDTSIDYLVGRTD 65
Cdd:COG1396  10 ERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGAD 71
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 4-60 4.96e-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: 62.19  E-value: 4.96e-15
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 505337243  4 QRIQDLRTDADLSQRELSEILHISQRSYSHYETGSRNIPIEMLIRLANYYDTSIDYL 60
Cdd:cd00093   2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
5-60 3.41e-14

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 59.84  E-value: 3.41e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 505337243    5 RIQDLRTDADLSQRELSEILHISQRSYSHYETGSRNIPIEMLIRLANYYDTSIDYL 60
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 6-60 1.12e-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: 56.01  E-value: 1.12e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 505337243   6 IQDLRTDADLSQRELSEILHISQRSYSHYETGSRNIPIEMLIRLANYYDTSIDYL 60
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 14-59 2.89e-05

addiction module antidote protein, HigA family; Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair. [Regulatory functions, DNA interactions, Regulatory functions, Protein interactions, Mobile and extrachromosomal element functions, Other]


Pssm-ID: 274228 [Multi-domain]  Cd Length: 78  Bit Score: 37.98  E-value: 2.89e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 505337243  14 DLSQRELSEILHISQRSYSHYETGSRNIPIEMLIRLANYYDTSIDY 59
Cdd:TIGR02607 18 GLSVRALAKALGVSRSTLSRIVNGRAAITADMALRLAKALGTSPEF 63
PRK08154 PRK08154
anaerobic benzoate catabolism transcriptional regulator; Reviewed
 4-62 3.03e-05

anaerobic benzoate catabolism transcriptional regulator; Reviewed


Pssm-ID: 236167 [Multi-domain]  Cd Length: 309  Bit Score: 39.55  E-value: 3.03e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 505337243   4 QRIQDLRTDADLSQRELSEILHISQRSYSHYETGSRNIPIEMLIRLANYYDTSIDYLVG 62
Cdd:PRK08154  31 ERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCSLADLLG 89
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
4-65 1.28e-17

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 69.26  E-value: 1.28e-17
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 505337243  4 QRIQDLRTDADLSQRELSEILHISQRSYSHYETGSRNIPIEMLIRLANYYDTSIDYLVGRTD 65
Cdd:COG1396  10 ERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGAD 71
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 4-60 4.96e-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: 62.19  E-value: 4.96e-15
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 505337243  4 QRIQDLRTDADLSQRELSEILHISQRSYSHYETGSRNIPIEMLIRLANYYDTSIDYL 60
Cdd:cd00093   2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
5-60 3.41e-14

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 59.84  E-value: 3.41e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 505337243    5 RIQDLRTDADLSQRELSEILHISQRSYSHYETGSRNIPIEMLIRLANYYDTSIDYL 60
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
4-65 8.00e-14

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 59.48  E-value: 8.00e-14
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 505337243  4 QRIQDLRTDADLSQRELSEILHISQRSYSHYETGSRNIPIEMLIRLANYYDTSIDYLVGRTD 65
Cdd:COG1476   7 NRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 6-60 1.12e-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: 56.01  E-value: 1.12e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 505337243   6 IQDLRTDADLSQRELSEILHISQRSYSHYETGSRNIPIEMLIRLANYYDTSIDYL 60
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 4-66 2.26e-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: 53.06  E-value: 2.26e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 505337243   4 QRIQDLRTDADLSQRELSEILHISQRSYSHYETGSRNIPIEMLIRLANYYDTSIDYLVGRTDR 66
Cdd:pfam12844  2 ERLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLLQGEGE 64
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 4-58 1.61e-09

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: 48.29  E-value: 1.61e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 505337243   4 QRIQDLRTDADLSQRELSEILHISQRSYSHYETGSRNIP-IEMLIRLANYYDTSID 58
Cdd:pfam13560  4 ARLRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGRPsPAVVERLARALGVDGA 59
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 4-59 3.61e-09

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: 3.61e-09
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 505337243  4 QRIQDLRTDADLSQRELSEILHISQRSYSHYETGSRNIPIEMLIRLANYYDTSIDY 59
Cdd:COG1813  15 ERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLAE 70
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 14-59 1.99e-07

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 43.64  E-value: 1.99e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 505337243 14 DLSQRELSEILHISQRSYSHYETGSRNIPIEMLIRLANYYDTSIDY 59
Cdd:COG3093  22 GLSQTELAKALGVSRQRISEILNGKRAITADTALRLARAFGTSAEF 67
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 4-67 4.91e-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: 42.70  E-value: 4.91e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 505337243  4 QRIQDLRTDADLSQRELSEILHISQRSYSHYETGSRNIPIEMLIRLANYYDTSIDYLVGRTDRK 67
Cdd:COG3620  20 EALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVLVVDDGK 83
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
4-50 1.85e-06

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 40.69  E-value: 1.85e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 505337243  4 QRIQDLRTDADLSQRELSEILHISQRSYSHYETGSRNI--PIEMLIRLA 50
Cdd:COG2944   9 EEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPsgAALKLLRLL 57
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 14-59 2.89e-05

addiction module antidote protein, HigA family; Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair. [Regulatory functions, DNA interactions, Regulatory functions, Protein interactions, Mobile and extrachromosomal element functions, Other]


Pssm-ID: 274228 [Multi-domain]  Cd Length: 78  Bit Score: 37.98  E-value: 2.89e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 505337243  14 DLSQRELSEILHISQRSYSHYETGSRNIPIEMLIRLANYYDTSIDY 59
Cdd:TIGR02607 18 GLSVRALAKALGVSRSTLSRIVNGRAAITADMALRLAKALGTSPEF 63
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 6-51 2.91e-05

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: 38.77  E-value: 2.91e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 505337243    6 IQDLRTDADLSQRELSEILHISQRSYSHYETGS--RNIPIEMLIRLAN 51
Cdd:TIGR03830  70 IRRIRKKLGLSQREAAELLGGGVNAFSRYERGEvrPSKALDKLLRLLD 117
PRK08154 PRK08154
anaerobic benzoate catabolism transcriptional regulator; Reviewed
 4-62 3.03e-05

anaerobic benzoate catabolism transcriptional regulator; Reviewed


Pssm-ID: 236167 [Multi-domain]  Cd Length: 309  Bit Score: 39.55  E-value: 3.03e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 505337243   4 QRIQDLRTDADLSQRELSEILHISQRSYSHYETGSRNIPIEMLIRLANYYDTSIDYLVG 62
Cdd:PRK08154  31 ERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCSLADLLG 89
COG1709 COG1709
Predicted transcriptional regulator,contains XRE-type HTH domain [Transcription];
10-42 2.50e-03

Predicted transcriptional regulator,contains XRE-type HTH domain [Transcription];


Pssm-ID: 441315  Cd Length: 234  Bit Score: 34.00  E-value: 2.50e-03
                         10        20        30
                 ....*....|....*....|....*....|...
gi 505337243  10 RTDADLSQRELSEILHISQRSYSHYETGSRNIP 42
Cdd:COG1709   31 REDFGISQTELARELGVSPSVISDYESGRRKSP 63
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH