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Conserved domains on  [gi|504355690|ref|WP_014542792|]
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HTH-type transcriptional regulator [Erwinia sp. Ejp617]

Protein Classification

transcriptional regulator( domain architecture ID 10793339)

helix-turn-helix-type transcriptional regulator

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK10072 PRK10072
HTH-type transcriptional regulator;
1-97 5.34e-54

HTH-type transcriptional regulator;


:

Pssm-ID: 182222  Cd Length: 96  Bit Score: 163.04  E-value: 5.34e-54
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504355690  1 METKDPMSELLSSLEQIVLtRDGIPAVIACKDSMAMPEPQRIREITGLKIDEFAQVLGVSVSSVKSWEAKRTKPSRSAQK 80
Cdd:PRK10072  1 MEYKDPMFELLSSLEQIVF-KDETQKITLTQKTTSFTEFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVKPSSAELK 79

                        90
                ....*....|....*..
gi 504355690 81 LMKLIQSNPYLSRDLLN 97
Cdd:PRK10072 80 LMRLIQANPALSKQLME 96
 
Name Accession Description Interval E-value
PRK10072 PRK10072
HTH-type transcriptional regulator;
1-97 5.34e-54

HTH-type transcriptional regulator;


Pssm-ID: 182222  Cd Length: 96  Bit Score: 163.04  E-value: 5.34e-54
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504355690  1 METKDPMSELLSSLEQIVLtRDGIPAVIACKDSMAMPEPQRIREITGLKIDEFAQVLGVSVSSVKSWEAKRTKPSRSAQK 80
Cdd:PRK10072  1 MEYKDPMFELLSSLEQIVF-KDETQKITLTQKTTSFTEFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVKPSSAELK 79

                        90
                ....*....|....*..
gi 504355690 81 LMKLIQSNPYLSRDLLN 97
Cdd:PRK10072 80 LMRLIQANPALSKQLME 96
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
31-91 4.92e-15

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 63.41  E-value: 4.92e-15
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 504355690 31 KDSMAMPEPQRIREITGLKIDEFAQVLGVSVSSVKSWEAKRTKPSRSAQKLMKLIQSNPYL 91
Cdd:COG2944   3 KKPLTPEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALKLLRLLEKHPEL 63
NadS NF041265
NadS family protein;
7-95 1.61e-11

NadS family protein;


Pssm-ID: 469165  Cd Length: 94  Bit Score: 55.18  E-value: 1.61e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504355690  7 MS---ELLSSLEQIVLTRDGI--PAVIACKDsmaMPEPQRIREITGLKIDEFAQVLGVSVSSVKSWEAKRTKPSRSAQKL 81
Cdd:NF041265  1 MSffdELKASLEEAVEIKNGVkaPARVTRYE---VADVKAIRAQLNVSQAEMAKALGTSVDTIKSWESKRRNPTGLAAKV 77

                        90
                ....*....|....
gi 504355690 82 MKLIQSNPYLSRDL 95
Cdd:NF041265 78 LATIQDNPAFFKEL 91
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 37-96 9.46e-08

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: 46.08  E-value: 9.46e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 504355690   37 PEPQRIREITGLKIDEFAQVLGVSVSSVKSWEAKRTKPSRSAQKLMKLIQSNPYLSRDLL 96
Cdd:TIGR03830  68 PEIRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSKALDKLLRLLDKHPELLEELR 127
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
40-86 6.19e-05

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 37.50  E-value: 6.19e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 504355690   40 QRIREITGLKIDEFAQVLGVSVSSVKSWEAKRTKPSRS-AQKLMKLIQ 86
Cdd:smart00530  3 KELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLEtLKKLAKALG 50
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 40-84 1.68e-04

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: 36.38  E-value: 1.68e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 504355690 40 QRIREITGLKIDEFAQVLGVSVSSVKSWEAKRTKPsrSAQKLMKL 84
Cdd:cd00093   5 KELRKEKGLTQEELAEKLGVSRSTISRIENGKRNP--SLETLEKL 47
MqsA_antitoxin pfam15731
Antitoxin component of bacterial toxin-antitoxin system, MqsA; MqsA_antitoxin is a family of ...
 2-97 7.01e-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: 36.20  E-value: 7.01e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504355690    2 ETKDPMSELLSSLEQIVLTRDGIPAVIAckdsmampepqRIREITGLKIDEFAQVLGVSVSSVKSWEAKRTKPSRSAQKL 81
Cdd:pfam15731  48 EEGDRYSALALAFNRQVNAVLIDPAFIA-----------RVRKKLGLDQREAAEIFGGGVNAFSRYENGKTRPPLALVKL 116

                          90
                  ....*....|....*.
gi 504355690   82 MKLIQSNPylsrDLLN 97
Cdd:pfam15731 117 LRLLDRHP----ELLE 128
 
Name Accession Description Interval E-value
PRK10072 PRK10072
HTH-type transcriptional regulator;
1-97 5.34e-54

HTH-type transcriptional regulator;


Pssm-ID: 182222  Cd Length: 96  Bit Score: 163.04  E-value: 5.34e-54
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504355690  1 METKDPMSELLSSLEQIVLtRDGIPAVIACKDSMAMPEPQRIREITGLKIDEFAQVLGVSVSSVKSWEAKRTKPSRSAQK 80
Cdd:PRK10072  1 MEYKDPMFELLSSLEQIVF-KDETQKITLTQKTTSFTEFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVKPSSAELK 79

                        90
                ....*....|....*..
gi 504355690 81 LMKLIQSNPYLSRDLLN 97
Cdd:PRK10072 80 LMRLIQANPALSKQLME 96
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
31-91 4.92e-15

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 63.41  E-value: 4.92e-15
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 504355690 31 KDSMAMPEPQRIREITGLKIDEFAQVLGVSVSSVKSWEAKRTKPSRSAQKLMKLIQSNPYL 91
Cdd:COG2944   3 KKPLTPEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALKLLRLLEKHPEL 63
NadS NF041265
NadS family protein;
7-95 1.61e-11

NadS family protein;


Pssm-ID: 469165  Cd Length: 94  Bit Score: 55.18  E-value: 1.61e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504355690  7 MS---ELLSSLEQIVLTRDGI--PAVIACKDsmaMPEPQRIREITGLKIDEFAQVLGVSVSSVKSWEAKRTKPSRSAQKL 81
Cdd:NF041265  1 MSffdELKASLEEAVEIKNGVkaPARVTRYE---VADVKAIRAQLNVSQAEMAKALGTSVDTIKSWESKRRNPTGLAAKV 77

                        90
                ....*....|....
gi 504355690 82 MKLIQSNPYLSRDL 95
Cdd:NF041265 78 LATIQDNPAFFKEL 91
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 37-96 9.46e-08

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: 46.08  E-value: 9.46e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 504355690   37 PEPQRIREITGLKIDEFAQVLGVSVSSVKSWEAKRTKPSRSAQKLMKLIQSNPYLSRDLL 96
Cdd:TIGR03830  68 PEIRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSKALDKLLRLLDKHPELLEELR 127
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
40-86 6.19e-05

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 37.50  E-value: 6.19e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 504355690   40 QRIREITGLKIDEFAQVLGVSVSSVKSWEAKRTKPSRS-AQKLMKLIQ 86
Cdd:smart00530  3 KELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLEtLKKLAKALG 50
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 40-84 1.68e-04

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: 36.38  E-value: 1.68e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 504355690 40 QRIREITGLKIDEFAQVLGVSVSSVKSWEAKRTKPsrSAQKLMKL 84
Cdd:cd00093   5 KELRKEKGLTQEELAEKLGVSRSTISRIENGKRNP--SLETLEKL 47
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 41-84 2.29e-04

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: 36.07  E-value: 2.29e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 504355690 41 RIREITGLKIDEFAQVLGVSVSSVKSWEAKRTKPSRS-AQKLMKL 84
Cdd:COG1813  19 EAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDtLRKLEKA 63
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 34-67 3.31e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 37.26  E-value: 3.31e-04
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 504355690  34 MAMPEPQRI----REITGLKIDEFAQVLGVSVSSVKSW 67
Cdd:PRK11924 124 DALPVKQREvfllRYVEGLSYREIAEILGVPVGTVKSR 161
MqsA_antitoxin pfam15731
Antitoxin component of bacterial toxin-antitoxin system, MqsA; MqsA_antitoxin is a family of ...
 2-97 7.01e-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: 36.20  E-value: 7.01e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504355690    2 ETKDPMSELLSSLEQIVLTRDGIPAVIAckdsmampepqRIREITGLKIDEFAQVLGVSVSSVKSWEAKRTKPSRSAQKL 81
Cdd:pfam15731  48 EEGDRYSALALAFNRQVNAVLIDPAFIA-----------RVRKKLGLDQREAAEIFGGGVNAFSRYENGKTRPPLALVKL 116

                          90
                  ....*....|....*.
gi 504355690   82 MKLIQSNPylsrDLLN 97
Cdd:pfam15731 117 LRLLDRHP----ELLE 128
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
34-84 2.53e-03

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 33.28  E-value: 2.53e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 504355690 34 MAMPEPQRIREI---TGLKIDEFAQVLGVSVSSVKSWEAKRTKPSRS-AQKLMKL 84
Cdd:COG1476   1 MKKKLGNRLKELrkeRGLTQEELAELLGVSRQTISAIENGKYNPSLElALKIARA 55
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 40-86 2.55e-03

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: 33.28  E-value: 2.55e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 504355690  40 QRIREITGLKIDEFAQVLGVSVSSVKSWEAKRTKPS-RSAQKLMKLIQ 86
Cdd:pfam01381  2 KELREELGLSQEELAEKLGVSRSTISKIENGKREPSlETLKKLAEALG 49
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 35-67 2.81e-03

DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 34.97  E-value: 2.81e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 504355690  35 AMPEPQRI----REITGLKIDEFAQVLGVSVSSVKSW 67
Cdd:COG1595  127 RLPPRQREvlvlRYLEGLSYAEIAEILGISEGTVKSR 163
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
40-84 3.18e-03

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 33.43  E-value: 3.18e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 504355690 40 QRIREITGLKIDEFAQVLGVSVSSVKSWEAKRTKPsrSAQKLMKL 84
Cdd:COG1396  13 RELRKARGLTQEELAERLGVSRSTISRIERGRRNP--SLETLLKL 55
 
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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