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Conserved domains on  [gi|1549660768|gb|RVJ73311|]
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XRE family transcriptional regulator [Sinorhizobium medicae]

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

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List of domain hits

 Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
7-76 1.14e-16

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 70.03  E-value: 1.14e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1549660768   7 NPIDAFVGSRVRMRRLMIGLSQEKLADGLGITFQQVQKYEKGTNRIGASRLQAIADILGVHPSFFFQQEE 76
Cdd:COG1396     2 STLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGAD 71
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
7-76 1.14e-16

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 70.03  E-value: 1.14e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1549660768   7 NPIDAFVGSRVRMRRLMIGLSQEKLADGLGITFQQVQKYEKGTNRIGASRLQAIADILGVHPSFFFQQEE 76
Cdd:COG1396     2 STLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGAD 71
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 14-71 1.24e-14

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: 64.11  E-value: 1.24e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1549660768  14 GSRVRMRRLMIGLSQEKLADGLGITFQQVQKYEKGTNRIGASRLQAIADILGVHPSFF 71
Cdd:cd00093     1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
16-71 2.03e-13

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 60.99  E-value: 2.03e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1549660768   16 RVRMRRLMIGLSQEKLADGLGITFQQVQKYEKGTNRIGASRLQAIADILGVHPSFF 71
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 17-71 2.26e-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: 58.32  E-value: 2.26e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1549660768  17 VRMRRLMIGLSQEKLADGLGITFQQVQKYEKGTNRIGASRLQAIADILGVHPSFF 71
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 13-96 1.20e-05

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 42.53  E-value: 1.20e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1549660768  13 VGSRVRMRRLMIGLSQEKLADGLGITFQQVQKYEKGTNRIGASRLQAIADILGVHPSFFFQQEEgsTQSGRPSGDIHESQ 92
Cdd:PRK09706    6 LGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCSPTWLLFGDE--DKQPTPPVPLNQPV 83


                  ....
gi 1549660768  93 EISS 96
Cdd:PRK09706   84 ELSE 87
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 13-65 1.68e-04

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: 37.64  E-value: 1.68e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1549660768  13 VGSRVRMRRLMIGLSQEKLADGLGITFQQVQKYEKGTNRIGASRLQAIADILG 65
Cdd:TIGR03070   3 IGILVRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDALG 55
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
7-76 1.14e-16

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 70.03  E-value: 1.14e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1549660768   7 NPIDAFVGSRVRMRRLMIGLSQEKLADGLGITFQQVQKYEKGTNRIGASRLQAIADILGVHPSFFFQQEE 76
Cdd:COG1396     2 STLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGAD 71
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 14-71 1.24e-14

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: 64.11  E-value: 1.24e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1549660768  14 GSRVRMRRLMIGLSQEKLADGLGITFQQVQKYEKGTNRIGASRLQAIADILGVHPSFF 71
Cdd:cd00093     1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
16-71 2.03e-13

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 60.99  E-value: 2.03e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1549660768   16 RVRMRRLMIGLSQEKLADGLGITFQQVQKYEKGTNRIGASRLQAIADILGVHPSFF 71
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 17-71 2.26e-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: 58.32  E-value: 2.26e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1549660768  17 VRMRRLMIGLSQEKLADGLGITFQQVQKYEKGTNRIGASRLQAIADILGVHPSFF 71
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
13-76 2.71e-12

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 58.32  E-value: 2.71e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1549660768  13 VGSRVRMRRLMIGLSQEKLADGLGITFQQVQKYEKGTNRIGASRLQAIADILGVHPSFFFQQEE 76
Cdd:COG1476     5 LGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 1-66 4.98e-12

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: 57.64  E-value: 4.98e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1549660768   1 MNKKDPNPIDAFVGSRVRMRRLMIGLSQEKLADGLGITFQQVQKYEKGTNRIGASRLQAIADILGV 66
Cdd:COG1813     1 MAKESTGELVEDYGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGI 66
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 14-75 5.81e-09

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: 49.59  E-value: 5.81e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1549660768  14 GSRVRMRRLMIGLSQEKLADGLGITFQQVQKYEKGTNRIGASRLQAIADILGVHPSFFFQQE 75
Cdd:pfam12844   1 GERLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLLQGE 62
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 13-77 5.04e-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: 45.40  E-value: 5.04e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1549660768  13 VGSRVRMRRLMIGLSQEKLADGLGITFQQVQKYEKGTNRIGASRLQAIADILGVHPSFFFQQEEG 77
Cdd:COG3620    18 LGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVLVVDDG 82
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 18-69 2.67e-06

Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to DNA.


Pssm-ID: 433211 [Multi-domain]  Cd Length: 63  Bit Score: 42.53  E-value: 2.67e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1549660768  18 RMRRLMI--GLSQEKLADGLGITFQQVQKYEKGT-NRIGASRLQAIADILGVHPS 69
Cdd:pfam13443   1 KLRKLMAdrGISKSDLARATGISRATLSRLRKGKpKRVSLDTLDKICDALGCQPG 55
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 13-96 1.20e-05

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 42.53  E-value: 1.20e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1549660768  13 VGSRVRMRRLMIGLSQEKLADGLGITFQQVQKYEKGTNRIGASRLQAIADILGVHPSFFFQQEEgsTQSGRPSGDIHESQ 92
Cdd:PRK09706    6 LGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCSPTWLLFGDE--DKQPTPPVPLNQPV 83


                  ....
gi 1549660768  93 EISS 96
Cdd:PRK09706   84 ELSE 87
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
1-71 2.31e-05

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 39.92  E-value: 2.31e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1549660768   1 MNKKDPNPIDafvgsrVRMRRLMIGLSQEKLADGLGITFQQVQKYEKGTNRIGASRLQAIAdILGVHPSFF 71
Cdd:COG2944     1 MTKKPLTPEE------IRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALKLLR-LLEKHPELL 64
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 14-69 5.50e-05

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: 39.05  E-value: 5.50e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1549660768  14 GSRVRMRRLMIGLSQEKLADGLGITFQQVQKYEKG-TNRIGASRLQAIADILGVHPS 69
Cdd:pfam13560   3 GARLRRLRERAGLSQEALARRLGVSRSTLSRLETGrRGRPSPAVVERLARALGVDGA 59
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 13-65 1.68e-04

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: 37.64  E-value: 1.68e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1549660768  13 VGSRVRMRRLMIGLSQEKLADGLGITFQQVQKYEKGTNRIGASRLQAIADILG 65
Cdd:TIGR03070   3 IGILVRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDALG 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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