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Conserved domains on  [gi|488288738|ref|WP_002359946|]
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MULTISPECIES: helix-turn-helix domain-containing protein [Enterococcus]

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];
7-83 4.78e-10

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 50.77  E-value: 4.78e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488288738  7 MQDVSKRLSRNLYMMMgtpredTKKIWKVSELSKASGVTPCVISRIKNdteGKEKPTIETVVKLAKALNVDPAELLK 83
Cdd:COG1396   1 MSTLKKALGERLRELR------KARGLTQEELAERLGVSRSTISRIER---GRRNPSLETLLKLAKALGVSLDELLG 68
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
7-83 4.78e-10

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 50.77  E-value: 4.78e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488288738  7 MQDVSKRLSRNLYMMMgtpredTKKIWKVSELSKASGVTPCVISRIKNdteGKEKPTIETVVKLAKALNVDPAELLK 83
Cdd:COG1396   1 MSTLKKALGERLRELR------KARGLTQEELAERLGVSRSTISRIER---GRRNPSLETLLKLAKALGVSLDELLG 68
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
33-81 1.90e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 45.97  E-value: 1.90e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 488288738   33 WKVSELSKASGVTPCVISRIKNdteGKEKPTIETVVKLAKALNVDPAEL 81
Cdd:smart00530 11 LTQEELAEKLGVSRSTLSRIEN---GKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 30-81 5.14e-08

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: 44.84  E-value: 5.14e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 488288738  30 KKIWKVSELSKASGVTPCVISRIKNdteGKEKPTIETVVKLAKALNVDPAEL 81
Cdd:pfam01381  7 ELGLSQEELAEKLGVSRSTISKIEN---GKREPSLETLKKLAEALGVSLDEL 55
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 30-81 7.07e-08

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: 44.47  E-value: 7.07e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 488288738 30 KKIWKVSELSKASGVTPCVISRIKNdteGKEKPTIETVVKLAKALNVDPAEL 81
Cdd:cd00093  10 EKGLTQEELAEKLGVSRSTISRIEN---GKRNPSLETLEKLAKALGVSLDEL 58
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 34-78 1.40e-03

addiction module antidote protein, HigA family; Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair. [Regulatory functions, DNA interactions, Regulatory functions, Protein interactions, Mobile and extrachromosomal element functions, Other]


Pssm-ID: 274228 [Multi-domain]  Cd Length: 78  Bit Score: 33.74  E-value: 1.40e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 488288738  34 KVSELSKASGVTPCVISRIKNdteGKEKPTIETVVKLAKALNVDP 78
Cdd:TIGR02607 20 SVRALAKALGVSRSTLSRIVN---GRAAITADMALRLAKALGTSP 61
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
7-83 4.78e-10

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 50.77  E-value: 4.78e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488288738  7 MQDVSKRLSRNLYMMMgtpredTKKIWKVSELSKASGVTPCVISRIKNdteGKEKPTIETVVKLAKALNVDPAELLK 83
Cdd:COG1396   1 MSTLKKALGERLRELR------KARGLTQEELAERLGVSRSTISRIER---GRRNPSLETLLKLAKALGVSLDELLG 68
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
33-81 1.90e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 45.97  E-value: 1.90e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 488288738   33 WKVSELSKASGVTPCVISRIKNdteGKEKPTIETVVKLAKALNVDPAEL 81
Cdd:smart00530 11 LTQEELAEKLGVSRSTLSRIEN---GKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 30-81 5.14e-08

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: 44.84  E-value: 5.14e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 488288738  30 KKIWKVSELSKASGVTPCVISRIKNdteGKEKPTIETVVKLAKALNVDPAEL 81
Cdd:pfam01381  7 ELGLSQEELAEKLGVSRSTISKIEN---GKREPSLETLKKLAEALGVSLDEL 55
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 30-81 7.07e-08

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: 44.47  E-value: 7.07e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 488288738 30 KKIWKVSELSKASGVTPCVISRIKNdteGKEKPTIETVVKLAKALNVDPAEL 81
Cdd:cd00093  10 EKGLTQEELAEKLGVSRSTISRIEN---GKRNPSLETLEKLAKALGVSLDEL 58
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 17-83 1.24e-07

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: 44.07  E-value: 1.24e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488288738  17 NLYMMMGTpredtKKIwKVSELSKASGVTPCVISRIKNDTegKEKPTIETVVKLAKALNVDPAELLK 83
Cdd:pfam13443  1 KLRKLMAD-----RGI-SKSDLARATGISRATLSRLRKGK--PKRVSLDTLDKICDALGCQPGDLLE 59
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
33-83 1.40e-06

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 41.28  E-value: 1.40e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 488288738 33 WKVSELSKASGVTPCVISRIKNDTEgkEKPTIETVVKLAKALNVDPAELLK 83
Cdd:COG3655  15 MTKKELAEATGISRATLSRLKNGKA--KAVRLDTLEKICKALDCQPGDLLE 63
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
37-82 3.93e-06

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 40.22  E-value: 3.93e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 488288738 37 ELSKASGVTPCVISRIKNdteGKEKPTIETVVKLAKALNVDPAELL 82
Cdd:COG1476  22 ELAELLGVSRQTISAIEN---GKYNPSLELALKIARALGVSLEELF 64
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 26-80 4.39e-05

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: 37.61  E-value: 4.39e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 488288738 26 REdtKKIWKVSELSKASGVTPCVISRIKNdteGKEKPTIETVVKLAKALNVDPAE 80
Cdd:COG1813  21 RE--ARGLSQEELAEKLGVSESTIRRIER---GEATPSLDTLRKLEKALGISLAE 70
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 33-82 8.86e-05

Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense mechanisms];


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 37.10  E-value: 8.86e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 488288738 33 WKVSELSKASGVTPCVISRIKNdteGKEKPTIETVVKLAKALNVDPAELL 82
Cdd:COG3093  23 LSQTELAKALGVSRQRISEILN---GKRAITADTALRLARAFGTSAEFWL 69
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 34-78 1.40e-03

addiction module antidote protein, HigA family; Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair. [Regulatory functions, DNA interactions, Regulatory functions, Protein interactions, Mobile and extrachromosomal element functions, Other]


Pssm-ID: 274228 [Multi-domain]  Cd Length: 78  Bit Score: 33.74  E-value: 1.40e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 488288738  34 KVSELSKASGVTPCVISRIKNdteGKEKPTIETVVKLAKALNVDP 78
Cdd:TIGR02607 20 SVRALAKALGVSRSTLSRIVN---GRAAITADMALRLAKALGTSP 61
 
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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