NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|506240193|ref|WP_015759968|]
View 

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

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
CxxCG_CxxCG_HTH super family cl37335
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 5-63 1.86e-16

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.


The actual alignment was detected with superfamily member TIGR03830:

Pssm-ID: 274805 [Multi-domain]  Cd Length: 127  Bit Score: 71.89  E-value: 1.86e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 506240193    5 LTAQDIKRIRRKYGLTQQGFARLLGLGEASVVRYENGQT-PSKANANLIRAADN-PAFMRD 63
Cdd:TIGR03830  65 LTGPEIRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVrPSKALDKLLRLLDKhPELLEE 125
 
Name Accession Description Interval E-value
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 5-63 1.86e-16

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: 71.89  E-value: 1.86e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 506240193    5 LTAQDIKRIRRKYGLTQQGFARLLGLGEASVVRYENGQT-PSKANANLIRAADN-PAFMRD 63
Cdd:TIGR03830  65 LTGPEIRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVrPSKALDKLLRLLDKhPELLEE 125
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
1-57 4.88e-13

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 61.10  E-value: 4.88e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 506240193   1 MSK-DLTAQDIKRIRRKYGLTQQGFARLLGLGEASVVRYENGQT-PSKANANLIRAADN 57
Cdd:COG2944    1 MTKkPLTPEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRkPSGAALKLLRLLEK 59
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 7-52 1.31e-05

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: 41.00  E-value: 1.31e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 506240193   7 AQDIKRIRRKYGLTQQGFARLLGLGEASVVRYENGQT-PSKANANLI 52
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRnPSLETLEKL 47
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
10-56 3.34e-05

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 39.81  E-value: 3.34e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 506240193    10 IKRIRRKYGLTQQGFARLLGLGEASVVRYENGQTPSKAnANLIRAAD 56
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSL-ETLKKLAK 47
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 10-52 7.02e-05

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: 39.06  E-value: 7.02e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 506240193   10 IKRIRRKYGLTQQGFARLLGLGEASVVRYENGQT-PSKANANLI 52
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKRePSLETLKKL 44
PRK10072 PRK10072
HTH-type transcriptional regulator;
9-66 5.79e-03

HTH-type transcriptional regulator;


Pssm-ID: 182222  Cd Length: 96  Bit Score: 34.77  E-value: 5.79e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 506240193   9 DIKRIRRKYGLTQQGFARLLGLGEASVVRYENGQT-PSKANANLIRAAD-NPAFMRDCFE 66
Cdd:PRK10072  37 EFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVkPSSAELKLMRLIQaNPALSKQLME 96
 
Name Accession Description Interval E-value
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 5-63 1.86e-16

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: 71.89  E-value: 1.86e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 506240193    5 LTAQDIKRIRRKYGLTQQGFARLLGLGEASVVRYENGQT-PSKANANLIRAADN-PAFMRD 63
Cdd:TIGR03830  65 LTGPEIRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVrPSKALDKLLRLLDKhPELLEE 125
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
1-57 4.88e-13

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 61.10  E-value: 4.88e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 506240193   1 MSK-DLTAQDIKRIRRKYGLTQQGFARLLGLGEASVVRYENGQT-PSKANANLIRAADN 57
Cdd:COG2944    1 MTKkPLTPEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRkPSGAALKLLRLLEK 59
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 7-52 1.31e-05

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: 41.00  E-value: 1.31e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 506240193   7 AQDIKRIRRKYGLTQQGFARLLGLGEASVVRYENGQT-PSKANANLI 52
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRnPSLETLEKL 47
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-52 2.48e-05

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 40.60  E-value: 2.48e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 506240193   1 MSKDLtAQDIKRIRRKYGLTQQGFARLLGLGEASVVRYENGQ-TPSKANANLI 52
Cdd:COG1476    1 MKKKL-GNRLKELRKERGLTQEELAELLGVSRQTISAIENGKyNPSLELALKI 52
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
10-56 3.34e-05

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 39.81  E-value: 3.34e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 506240193    10 IKRIRRKYGLTQQGFARLLGLGEASVVRYENGQTPSKAnANLIRAAD 56
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSL-ETLKKLAK 47
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 10-52 7.02e-05

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: 39.06  E-value: 7.02e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 506240193   10 IKRIRRKYGLTQQGFARLLGLGEASVVRYENGQT-PSKANANLI 52
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKRePSLETLKKL 44
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-55 1.52e-04

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 38.82  E-value: 1.52e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 506240193   1 MSKDLT--AQDIKRIRRKYGLTQQGFARLLGLGEASVVRYENGQT-PSKANANLIRAA 55
Cdd:COG1396    1 MSTLKKalGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRnPSLETLLKLAKA 58
MqsA_antitoxin pfam15731
Antitoxin component of bacterial toxin-antitoxin system, MqsA; MqsA_antitoxin is a family of ...
 9-56 8.66e-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: 37.74  E-value: 8.66e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 506240193    9 DIKRIRRKYGLTQQGFARLLGLGEASVVRYENGQT-PSKANANLIRAAD 56
Cdd:pfam15731  73 FIARVRKKLGLDQREAAEIFGGGVNAFSRYENGKTrPPLALVKLLRLLD 121
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 7-51 1.32e-03

transcriptional regulator, y4mF family; Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems. [Regulatory functions, DNA interactions]


Pssm-ID: 213767 [Multi-domain]  Cd Length: 58  Bit Score: 35.71  E-value: 1.32e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 506240193    7 AQDIKRIRRKYGLTQQGFARLLGLGEASVVRYENGqtpsKANANL 51
Cdd:TIGR03070   4 GILVRARRKALGLTQADLADLAGVGLRFIRDLENG----KPTVRL 44
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 10-56 1.66e-03

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: 35.58  E-value: 1.66e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 506240193   10 IKRIRRKYGLTQQGFARLLGLGEASVVRYENGQTPSKANANLIRAAD 56
Cdd:pfam13560   6 LRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGRPSPAVVERLAR 52
PRK10072 PRK10072
HTH-type transcriptional regulator;
9-66 5.79e-03

HTH-type transcriptional regulator;


Pssm-ID: 182222  Cd Length: 96  Bit Score: 34.77  E-value: 5.79e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 506240193   9 DIKRIRRKYGLTQQGFARLLGLGEASVVRYENGQT-PSKANANLIRAAD-NPAFMRDCFE 66
Cdd:PRK10072  37 EFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVkPSSAELKLMRLIQaNPALSKQLME 96
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 4-43 6.09e-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: 34.61  E-value: 6.09e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 506240193   4 DLTAQDIKRIRRKYGLTQQGFARLLGLGEASVVRYENGQT 43
Cdd:COG3620   16 DTLGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKR 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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH