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Conserved domains on  [gi|496091426|ref|WP_008815933|]
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MULTISPECIES: helix-turn-helix transcriptional regulator [Enterobacterales]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 10650117)

helix-turn-helix (HTH) domain-containing protein with an XRE (Xenobiotic Response Element) family HTH domain, binds DNA and may function as a transcriptional regulator

CATH:  1.10.10.10
Gene Ontology:  GO:0003677
PubMed:  15808743|2644244|8831795
SCOP:  4000362

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
5-64 4.26e-12

Helix-turn-helix XRE-family like proteins;


:

Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 56.37  E-value: 4.26e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 496091426     5 RLREAREAAGISQEKLSQLIDIdgknSRSRLSSYEVGRTEPPFSLVVKIARLLDYPEYYF 64
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGV----SRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
 
Name Accession Description Interval E-value
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
5-64 4.26e-12

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 56.37  E-value: 4.26e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 496091426     5 RLREAREAAGISQEKLSQLIDIdgknSRSRLSSYEVGRTEPPFSLVVKIARLLDYPEYYF 64
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGV----SRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-70 6.78e-12

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 56.54  E-value: 6.78e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496091426   1 MVPKRLREAREAAGISQEKLSQLIDIdgknSRSRLSSYEVGRTEPPFSLVVKIARLLDYPEYYFYTVDDD 70
Cdd:COG1396    7 ALGERLRELRKARGLTQEELAERLGV----SRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADE 72
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 4-64 1.46e-11

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: 55.25  E-value: 1.46e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 496091426   4 KRLREAREAAGISQEKLSQLIDIdgknSRSRLSSYEVGRTEPPFSLVVKIARLLDYPEYYF 64
Cdd:cd00093    2 ERLKELRKEKGLTQEELAEKLGV----SRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 6-64 2.24e-10

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: 52.16  E-value: 2.24e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 496091426    6 LREAREAAGISQEKLSQLIDIdgknSRSRLSSYEVGRTEPPFSLVVKIARLLDYPEYYF 64
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGV----SRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
PRK13355 PRK13355
bifunctional HTH-domain containing protein/aminotransferase; Provisional
 5-63 1.16e-04

bifunctional HTH-domain containing protein/aminotransferase; Provisional


Pssm-ID: 237361 [Multi-domain]  Cd Length: 517  Bit Score: 40.11  E-value: 1.16e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 496091426   5 RLREAREAAGISQEKLSQLIDIDG-KNSRSRLSSYEVGRTEPPFSLVVKIARLLDYPEYY 63
Cdd:PRK13355   7 RLKQAMKARGLKQEDLVHAAEARGvKLGKSHISQYVSGKTGPRRDVLPFLAAILGVSEDW 66
 
Name Accession Description Interval E-value
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
5-64 4.26e-12

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 56.37  E-value: 4.26e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 496091426     5 RLREAREAAGISQEKLSQLIDIdgknSRSRLSSYEVGRTEPPFSLVVKIARLLDYPEYYF 64
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGV----SRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-70 6.78e-12

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 56.54  E-value: 6.78e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496091426   1 MVPKRLREAREAAGISQEKLSQLIDIdgknSRSRLSSYEVGRTEPPFSLVVKIARLLDYPEYYFYTVDDD 70
Cdd:COG1396    7 ALGERLRELRKARGLTQEELAERLGV----SRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADE 72
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 4-64 1.46e-11

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: 55.25  E-value: 1.46e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 496091426   4 KRLREAREAAGISQEKLSQLIDIdgknSRSRLSSYEVGRTEPPFSLVVKIARLLDYPEYYF 64
Cdd:cd00093    2 ERLKELRKEKGLTQEELAEKLGV----SRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-69 2.70e-11

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 54.85  E-value: 2.70e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 496091426   1 MVPKRLREAREAAGISQEKLSQLIDIdgknSRSRLSSYEVGRTEPPFSLVVKIARLLDYPEYYFYTVDD 69
Cdd:COG1476    4 KLGNRLKELRKERGLTQEELAELLGV----SRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 6-64 2.24e-10

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: 52.16  E-value: 2.24e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 496091426    6 LREAREAAGISQEKLSQLIDIdgknSRSRLSSYEVGRTEPPFSLVVKIARLLDYPEYYF 64
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGV----SRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 4-70 3.71e-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: 51.91  E-value: 3.71e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 496091426    4 KRLREAREAAGISQEKLSQLIDIdgknSRSRLSSYEVGRTEPPFSLVVKIARLLDYPEYYFYTVDDD 70
Cdd:pfam12844   2 ERLRKAREERGLTQEELAERLGI----SRSQLSAIENGKSVPPAETLYKIAELLGVPANWLLQGEGE 64
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 2-58 6.63e-10

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: 51.09  E-value: 6.63e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 496091426   2 VPKRLREAREAAGISQEKLSQLIDIdgknSRSRLSSYEVGRTEPPFSLVVKIARLLD 58
Cdd:COG1813   13 YGERIREAREARGLSQEELAEKLGV----SESTIRRIERGEATPSLDTLRKLEKALG 65
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 5-58 1.26e-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: 42.52  E-value: 1.26e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 496091426    5 RLREAREAAGISQEKLSQLIDIdgknSRSRLSSYEVGRTE-PPFSLVVKIARLLD 58
Cdd:pfam13560   5 RLRRLRERAGLSQEALARRLGV----SRSTLSRLETGRRGrPSPAVVERLARALG 55
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 2-70 2.24e-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: 42.70  E-value: 2.24e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 496091426   2 VPKRLREAREAAGISQEKLSQLIDIdgknSRSRLSSYEVGRTEPPFSLVVKIARLLDYPEYYFYTVDDD 70
Cdd:COG3620   18 LGEALRLMRKELGLSQLPVAELVGV----SQSDILRIESGKRDPTVSTLEKIAEALGKELSAVLVVDDG 82
PRK13355 PRK13355
bifunctional HTH-domain containing protein/aminotransferase; Provisional
 5-63 1.16e-04

bifunctional HTH-domain containing protein/aminotransferase; Provisional


Pssm-ID: 237361 [Multi-domain]  Cd Length: 517  Bit Score: 40.11  E-value: 1.16e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 496091426   5 RLREAREAAGISQEKLSQLIDIDG-KNSRSRLSSYEVGRTEPPFSLVVKIARLLDYPEYY 63
Cdd:PRK13355   7 RLKQAMKARGLKQEDLVHAAEARGvKLGKSHISQYVSGKTGPRRDVLPFLAAILGVSEDW 66
MqsA_antitoxin pfam15731
Antitoxin component of bacterial toxin-antitoxin system, MqsA; MqsA_antitoxin is a family of ...
 3-61 6.53e-04

Antitoxin component of bacterial toxin-antitoxin system, MqsA; MqsA_antitoxin is a family of prokaryotic proteins that act as antidotes to the mRNA interferase MqsR. It has a zinc-binding at the very N-terminus indicating its DNA-binding capacity. MqsR is the gene most highly upregulated in E. Colo MqsR_toxin is a family of bacterial toxins that act as an mRNA interferase. MqsR is the gene most highly upregulated in E. coli persister cells and it plays an essential role in biofilm regulation and cell signalling. It forms part of a bacterial toxin-antitoxin TA system, and as expected for a TA system, the expression of the MqsR toxin leads to growth arrest, while co-expression with its antitoxin, MqsA, rescues the growth arrest phenotype. In addition, MqsR associates with MqsA to form a tight, non-toxic complex and both MqsA alone and the MqsR:MqsA2:MqsR complex bind and regulate the mqsR promoter. The structure of MqsR shows that is is a member of the RelE/YoeB family of bacterial RNases that are structurally and functionally characterized bacterial toxins.


Pssm-ID: 292359 [Multi-domain]  Cd Length: 131  Bit Score: 36.97  E-value: 6.53e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 496091426    3 PKRLREAREAAGISQEKLSQLIDIdGKNSRSRlssYEVGRTEPPFSLvVKIARLLD-YPE 61
Cdd:pfam15731  71 PAFIARVRKKLGLDQREAAEIFGG-GVNAFSR---YENGKTRPPLAL-VKLLRLLDrHPE 125
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 4-61 3.88e-03

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: 33.62  E-value: 3.88e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 496091426   4 KRLREAREAAGISQEKLSQLIDIdgknSRSRLSSYEVGRTE----PPFS--LVVKIARLLDYPE 61
Cdd:COG1426    8 ELLRQAREAKGLSLEDVAERTKI----SVSYLEAIEEGDFDalpgPVYVrgFLRSYARALGLDP 67
 
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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