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Conserved domains on  [gi|447055151|ref|WP_001132407|]
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MULTISPECIES: DNA-binding transcriptional regulator [Enterobacteriaceae]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 11459264)

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
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
6-69 2.93e-09

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


:

Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 48.01  E-value: 2.93e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 447055151  6 TPENIKRLRQKIGLTQKECAEIFSMSPRTWRRKEEPVGTASGTALTpvefkfLLLLAGEHPDYV 69
Cdd:COG2944   7 TPEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALK------LLRLLEKHPELL 64
 
Name Accession Description Interval E-value
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
6-69 2.93e-09

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 48.01  E-value: 2.93e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 447055151  6 TPENIKRLRQKIGLTQKECAEIFSMSPRTWRRKEEPVGTASGTALTpvefkfLLLLAGEHPDYV 69
Cdd:COG2944   7 TPEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALK------LLRLLEKHPELL 64
Xre-like-HTH pfam20432
Antitoxin Xre-like helix-turn-helix domain; This entry represents the N-terminal domain of the ...
 10-63 1.15e-06

Antitoxin Xre-like helix-turn-helix domain; This entry represents the N-terminal domain of the antitoxin component Xre of a type II toxin-antitoxin (TA) system, which is the helix-turn-helix (HTH) DNA binding domain, structurally similar to the Cro repressor, therefore, also referred to as HTH/Cro-like DNA-binding domain. This domain is also found in other antitoxin components, associated with a C-terminal toxin-binding domain pfam09722.


Pssm-ID: 466581  Cd Length: 57  Bit Score: 41.39  E-value: 1.15e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 447055151  10 IKRLRQKIGLTQKECAEIFSMSPRTWRRKEepvgtASGTALTPVEFKFLLLLAG 63
Cdd:pfam20432  9 VLRLAEALGLTDEELAELLGLSRSTLSRKR-----KENGRLSPDESERLLRLAR 57
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 6-68 2.99e-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: 39.15  E-value: 2.99e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 447055151    6 TPENIKRLRQKIGLTQKECAEIFSMSPRTWRRKEepvgtaSGTALTPVEFKFLLLLAGEHPDY 68
Cdd:TIGR03830  66 TGPEIRRIRKKLGLSQREAAELLGGGVNAFSRYE------RGEVRPSKALDKLLRLLDKHPEL 122
VC1465_fam NF040522
VC1465 family Xer recombination activation factor;
10-63 7.73e-05

VC1465 family Xer recombination activation factor;


Pssm-ID: 439737 [Multi-domain]  Cd Length: 111  Bit Score: 37.81  E-value: 7.73e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 447055151  10 IKRLRQKIGLTQKECAEIFSMSPRTWRRKEepvgtasgTALTPVE---FKFLLLLAG 63
Cdd:NF040522   1 IKETREKAGLTRQQAAEMLRVSLRTVQNWE--------TGKVPMPycaFKLERRLIP 49
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
9-37 1.33e-03

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 33.65  E-value: 1.33e-03
                          10        20
                  ....*....|....*....|....*....
gi 447055151    9 NIKRLRQKIGLTQKECAEIFSMSPRTWRR 37
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSR 29
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 8-37 1.64e-03

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: 33.30  E-value: 1.64e-03
                        10        20        30
                ....*....|....*....|....*....|
gi 447055151  8 ENIKRLRQKIGLTQKECAEIFSMSPRTWRR 37
Cdd:cd00093   2 ERLKELRKEKGLTQEELAEKLGVSRSTISR 31
 
Name Accession Description Interval E-value
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
6-69 2.93e-09

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 48.01  E-value: 2.93e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 447055151  6 TPENIKRLRQKIGLTQKECAEIFSMSPRTWRRKEEPVGTASGTALTpvefkfLLLLAGEHPDYV 69
Cdd:COG2944   7 TPEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALK------LLRLLEKHPELL 64
Xre-like-HTH pfam20432
Antitoxin Xre-like helix-turn-helix domain; This entry represents the N-terminal domain of the ...
 10-63 1.15e-06

Antitoxin Xre-like helix-turn-helix domain; This entry represents the N-terminal domain of the antitoxin component Xre of a type II toxin-antitoxin (TA) system, which is the helix-turn-helix (HTH) DNA binding domain, structurally similar to the Cro repressor, therefore, also referred to as HTH/Cro-like DNA-binding domain. This domain is also found in other antitoxin components, associated with a C-terminal toxin-binding domain pfam09722.


Pssm-ID: 466581  Cd Length: 57  Bit Score: 41.39  E-value: 1.15e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 447055151  10 IKRLRQKIGLTQKECAEIFSMSPRTWRRKEepvgtASGTALTPVEFKFLLLLAG 63
Cdd:pfam20432  9 VLRLAEALGLTDEELAELLGLSRSTLSRKR-----KENGRLSPDESERLLRLAR 57
MqsA_antitoxin pfam15731
Antitoxin component of bacterial toxin-antitoxin system, MqsA; MqsA_antitoxin is a family of ...
 7-67 2.43e-06

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: 41.98  E-value: 2.43e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 447055151    7 PENIKRLRQKIGLTQKECAEIFSMSPRTWRRKEepvgtaSGTALTPVEFKFLLLLAGEHPD 67
Cdd:pfam15731  71 PAFIARVRKKLGLDQREAAEIFGGGVNAFSRYE------NGKTRPPLALVKLLRLLDRHPE 125
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 6-68 2.99e-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: 39.15  E-value: 2.99e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 447055151    6 TPENIKRLRQKIGLTQKECAEIFSMSPRTWRRKEepvgtaSGTALTPVEFKFLLLLAGEHPDY 68
Cdd:TIGR03830  66 TGPEIRRIRKKLGLSQREAAELLGGGVNAFSRYE------RGEVRPSKALDKLLRLLDKHPEL 122
VC1465_fam NF040522
VC1465 family Xer recombination activation factor;
10-63 7.73e-05

VC1465 family Xer recombination activation factor;


Pssm-ID: 439737 [Multi-domain]  Cd Length: 111  Bit Score: 37.81  E-value: 7.73e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 447055151  10 IKRLRQKIGLTQKECAEIFSMSPRTWRRKEepvgtasgTALTPVE---FKFLLLLAG 63
Cdd:NF040522   1 IKETREKAGLTRQQAAEMLRVSLRTVQNWE--------TGKVPMPycaFKLERRLIP 49
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
8-39 3.45e-04

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 35.74  E-value: 3.45e-04
                        10        20        30
                ....*....|....*....|....*....|..
gi 447055151  8 ENIKRLRQKIGLTQKECAEIFSMSPRTWRRKE 39
Cdd:COG1396  10 ERLRELRKARGLTQEELAERLGVSRSTISRIE 41
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
9-37 1.33e-03

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 33.65  E-value: 1.33e-03
                          10        20
                  ....*....|....*....|....*....
gi 447055151    9 NIKRLRQKIGLTQKECAEIFSMSPRTWRR 37
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSR 29
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
8-39 1.36e-03

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 33.67  E-value: 1.36e-03
                        10        20        30
                ....*....|....*....|....*....|..
gi 447055151  8 ENIKRLRQKIGLTQKECAEIFSMSPRTWRRKE 39
Cdd:COG1476   7 NRLKELRKERGLTQEELAELLGVSRQTISAIE 38
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 4-37 1.42e-03

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: 33.76  E-value: 1.42e-03
                        10        20        30
                ....*....|....*....|....*....|....
gi 447055151  4 ENTPENIKRLRQKIGLTQKECAEIFSMSPRTWRR 37
Cdd:COG1813  11 EDYGERIREAREARGLSQEELAEKLGVSESTIRR 44
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 8-37 1.64e-03

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: 33.30  E-value: 1.64e-03
                        10        20        30
                ....*....|....*....|....*....|
gi 447055151  8 ENIKRLRQKIGLTQKECAEIFSMSPRTWRR 37
Cdd:cd00093   2 ERLKELRKEKGLTQEELAEKLGVSRSTISR 31
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 2-40 4.09e-03

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: 33.07  E-value: 4.09e-03
                        10        20        30
                ....*....|....*....|....*....|....*....
gi 447055151  2 PNENTPENIKRLRQKIGLTQKECAEIFSMSPRTWRRKEE 40
Cdd:COG3620  14 PDDTLGEALRLMRKELGLSQLPVAELVGVSQSDILRIES 52
 
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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