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Conserved domains on  [gi|340707908|pdb|3QQ6|B]
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Chain B, HTH-type transcriptional regulator sinR

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];
10-77 1.54e-20

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 76.96  E-value: 1.54e-20
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|....*...
3QQ6_B      10 MIGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNlQTNPSIQFLEKVSAVLDVSVHTLLDEKHET 77
Cdd:COG1396  7 ALGERLRELRKARGLTQEELAERLGVSRSTISRIERG-RRNPSLETLLKLAKALGVSLDELLGGADEE 73
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
10-77 1.54e-20

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 76.96  E-value: 1.54e-20
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|....*...
3QQ6_B      10 MIGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNlQTNPSIQFLEKVSAVLDVSVHTLLDEKHET 77
Cdd:COG1396  7 ALGERLRELRKARGLTQEELAERLGVSRSTISRIERG-RRNPSLETLLKLAKALGVSLDELLGGADEE 73
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 12-70 3.75e-15

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: 62.57  E-value: 3.75e-15
                       10        20        30        40        50
               ....*....|....*....|....*....|....*....|....*....|....*....
3QQ6_B      12 GQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNlQTNPSIQFLEKVSAVLDVSVHTL 70
Cdd:cd00093  1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENG-KRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
14-67 7.56e-15

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 61.77  E-value: 7.56e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
3QQ6_B         14 RIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNlQTNPSIQFLEKVSAVLDVSV 67
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENG-KRKPSLETLKKLAKALGVSL 53
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 15-70 1.62e-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: 56.01  E-value: 1.62e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
3QQ6_B        15 IKQYRKEKGYSLSELAEKAGVAKSYLSSIERNlQTNPSIQFLEKVSAVLDVSVHTL 70
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENG-KREPSLETLKKLAEALGVSLDEL 55
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 10-65 9.51e-07

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: 41.49  E-value: 9.51e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
3QQ6_B        10 MIGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIErnlQTNPSIQfLEKVSAVLDV 65
Cdd:TIGR03070  2 QIGILVRARRKALGLTQADLADLAGVGLRFIRDLE---NGKPTVR-LDKVLRVLDA 53
PRK13890 PRK13890
conjugal transfer protein TrbA; Provisional
 21-72 9.86e-07

conjugal transfer protein TrbA; Provisional


Pssm-ID: 237547 [Multi-domain]  Cd Length: 120  Bit Score: 42.82  E-value: 9.86e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
3QQ6_B        21 EKGYSLSELAEKAGVAKSYLSSIERNlQTNPSIQFLEKVSAVLDVSVHTLLD 72
Cdd:PRK13890  16 ERHMTKKELSERSGVSISFLSDLTTG-KANPSLKVMEAIADALETPLPLLLE 66
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
10-77 1.54e-20

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 76.96  E-value: 1.54e-20
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|....*...
3QQ6_B      10 MIGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNlQTNPSIQFLEKVSAVLDVSVHTLLDEKHET 77
Cdd:COG1396  7 ALGERLRELRKARGLTQEELAERLGVSRSTISRIERG-RRNPSLETLLKLAKALGVSLDELLGGADEE 73
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
10-74 8.60e-17

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 67.18  E-value: 8.60e-17
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|....*
3QQ6_B      10 MIGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNlQTNPSIQFLEKVSAVLDVSVHTLLDEK 74
Cdd:COG1476  4 KLGNRLKELRKERGLTQEELAELLGVSRQTISAIENG-KYNPSLELALKIARALGVSLEELFSLE 67
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 12-70 3.75e-15

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: 62.57  E-value: 3.75e-15
                       10        20        30        40        50
               ....*....|....*....|....*....|....*....|....*....|....*....
3QQ6_B      12 GQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNlQTNPSIQFLEKVSAVLDVSVHTL 70
Cdd:cd00093  1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENG-KRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
14-67 7.56e-15

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 61.77  E-value: 7.56e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
3QQ6_B         14 RIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNlQTNPSIQFLEKVSAVLDVSV 67
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENG-KRKPSLETLKKLAKALGVSL 53
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 11-66 4.17e-13

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: 58.03  E-value: 4.17e-13
                       10        20        30        40        50
               ....*....|....*....|....*....|....*....|....*....|....*.
3QQ6_B      11 IGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNlQTNPSIQFLEKVSAVLDVS 66
Cdd:COG1813 13 YGERIREAREARGLSQEELAEKLGVSESTIRRIERG-EATPSLDTLRKLEKALGIS 67
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 15-70 1.62e-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: 56.01  E-value: 1.62e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
3QQ6_B        15 IKQYRKEKGYSLSELAEKAGVAKSYLSSIERNlQTNPSIQFLEKVSAVLDVSVHTL 70
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENG-KREPSLETLKKLAEALGVSLDEL 55
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 11-71 3.61e-10

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: 51.17  E-value: 3.61e-10
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|.
3QQ6_B      11 IGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNlQTNPSIQFLEKVSAVLDVSVHTLL 71
Cdd:COG3620 18 LGEALRLMRKELGLSQLPVAELVGVSQSDILRIESG-KRDPTVSTLEKIAEALGKELSAVL 77
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 11-68 1.07e-09

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: 49.06  E-value: 1.07e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
3QQ6_B        11 IGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAVLDVSVH 68
Cdd:pfam13560  2 LGARLRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGRPSPAVVERLARALGVDGA 59
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 11-46 5.28e-09

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: 47.49  E-value: 5.28e-09
                       10        20        30
               ....*....|....*....|....*....|....*.
3QQ6_B      11 IGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERN 46
Cdd:COG1426  6 IGELLRQAREAKGLSLEDVAERTKISVSYLEAIEEG 41
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 12-71 1.04e-08

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: 46.51  E-value: 1.04e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
3QQ6_B        12 GQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNlQTNPSIQFLEKVSAVLDVSVHTLL 71
Cdd:pfam12844  1 GERLRKAREERGLTQEELAERLGISRSQLSAIENG-KSVPPAETLYKIAELLGVPANWLL 59
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
10-72 2.32e-07

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 43.21  E-value: 2.32e-07
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|...
3QQ6_B      10 MIGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAVLDVSVHTLLD 72
Cdd:COG3655  1 MIYVKLDELLAERGMTKKELAEATGISRATLSRLKNGKAKAVRLDTLEKICKALDCQPGDLLE 63
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 10-65 9.51e-07

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: 41.49  E-value: 9.51e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
3QQ6_B        10 MIGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIErnlQTNPSIQfLEKVSAVLDV 65
Cdd:TIGR03070  2 QIGILVRARRKALGLTQADLADLAGVGLRFIRDLE---NGKPTVR-LDKVLRVLDA 53
PRK13890 PRK13890
conjugal transfer protein TrbA; Provisional
 21-72 9.86e-07

conjugal transfer protein TrbA; Provisional


Pssm-ID: 237547 [Multi-domain]  Cd Length: 120  Bit Score: 42.82  E-value: 9.86e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
3QQ6_B        21 EKGYSLSELAEKAGVAKSYLSSIERNlQTNPSIQFLEKVSAVLDVSVHTLLD 72
Cdd:PRK13890  16 ERHMTKKELSERSGVSISFLSDLTTG-KANPSLKVMEAIADALETPLPLLLE 66
PRK08154 PRK08154
anaerobic benzoate catabolism transcriptional regulator; Reviewed
 10-71 5.34e-06

anaerobic benzoate catabolism transcriptional regulator; Reviewed


Pssm-ID: 236167 [Multi-domain]  Cd Length: 309  Bit Score: 41.86  E-value: 5.34e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
3QQ6_B        10 MIGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNlQTNPSIQFLEKVSAVLDVSVHTLL 71
Cdd:PRK08154  28 ALGERVRTLRARRGMSRKVLAQASGVSERYLAQLESG-QGNVSILLLRRVARALGCSLADLL 88
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
10-78 7.60e-06

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 41.32  E-value: 7.60e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
3QQ6_B        10 MIGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNlQTNPSIQFLEKVSAVLDVSVHTLLDEKHETE 78
Cdd:PRK09943   7 APGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQD-KVSPAISTLQKLLKVYGLSLSEFFSEPEKPD 74
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 14-72 1.92e-05

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: 38.29  E-value: 1.92e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
3QQ6_B        14 RIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAVLDVSVHTLLD 72
Cdd:pfam13443  1 KLRKLMADRGISKSDLARATGISRATLSRLRKGKPKRVSLDTLDKICDALGCQPGDLLE 59
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 10-71 1.22e-04

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 37.53  E-value: 1.22e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
3QQ6_B        10 MIGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNlQTNPSIQFLEKVSAVLDVSVHTLL 71
Cdd:PRK09706   5 TLGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERD-ETEPTGKNLFALAKALQCSPTWLL 65
PRK04140 PRK04140
transcriptional regulator;
12-65 1.10e-03

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 35.60  E-value: 1.10e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
3QQ6_B        12 GQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQtNPSIQFLEKVSAVLDV 65
Cdd:PRK04140 128 GDVLREAREELGLSLGELASELGVSRRTISKYENGGM-NASIEVAIKLEEILDV 180
COG1395 COG1395
Predicted transcriptional regulator [Transcription];
12-53 1.34e-03

Predicted transcriptional regulator [Transcription];


Pssm-ID: 441005 [Multi-domain]  Cd Length: 313  Bit Score: 35.20  E-value: 1.34e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
3QQ6_B       12 GQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNlQTNPSI 53
Cdd:COG1395 129 GEKLRELREERGLSLGELASELGVSRRTISKYERG-EMDASI 169
 
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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