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Conserved domains on  [gi|1608035124|gb|QBX07274|]
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hypothetical protein JavanS13_0017 [Streptococcus satellite phage Javan13]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 10007659)

helix-turn-helix (HTH) domain-containing protein with an XRE (Xenobiotic Response Element) family HTH domain, binds DNA and may function as a transcriptional regulator

CATH:  1.10.10.10
Gene Ontology:  GO:0003677
PubMed:  15808743|2644244|8831795
SCOP:  4000362

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
1-53 3.06e-10

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


:

Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 49.37  E-value: 3.06e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 1608035124  1 MVKNNLHIVMALNNTKASEVAEKTGISKSTISKFINGKTD-IKLSTLISLCIFF 53
Cdd:COG3655    1 MIYVKLDELLAERGMTKKELAEATGISRATLSRLKNGKAKaVRLDTLEKICKAL 54
 
Name Accession Description Interval E-value
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
1-53 3.06e-10

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 49.37  E-value: 3.06e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 1608035124  1 MVKNNLHIVMALNNTKASEVAEKTGISKSTISKFINGKTD-IKLSTLISLCIFF 53
Cdd:COG3655    1 MIYVKLDELLAERGMTKKELAEATGISRATLSRLKNGKAKaVRLDTLEKICKAL 54
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
18-53 3.71e-09

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 46.36  E-value: 3.71e-09
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1608035124  18 SEVAEKTGISKSTISKFINGKTDIKLSTLISLCIFF 53
Cdd:smart00530 14 EELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKAL 49
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 18-53 8.52e-09

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: 45.62  E-value: 8.52e-09
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 1608035124 18 SEVAEKTGISKSTISKFINGKTDIKLSTLISLCIFF 53
Cdd:cd00093   16 EELAEKLGVSRSTISRIENGKRNPSLETLEKLAKAL 51
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 5-53 2.83e-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: 41.76  E-value: 2.83e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 1608035124  5 NLHIVMALNNTKASEVAEKTGISKSTISKFINGKTD-IKLSTLISLCIFF 53
Cdd:pfam13443  1 KLRKLMADRGISKSDLARATGISRATLSRLRKGKPKrVSLDTLDKICDAL 50
lysogeny_AimR NF038310
AimR family lysis-lysogeny pheromone receptor; The founding member of this family, AimR ...
 6-47 3.15e-05

AimR family lysis-lysogeny pheromone receptor; The founding member of this family, AimR (arbitrium receptor), is a DNA-binding phage regulatory protein that acts as a receptor for a 6-amino acid signaling peptide cleaved from the C-terminus of AimP. AimR controls expression of AimX, the third member of the quorum sensing-like arbitrium system and an inhibitor of phage lysogeny.


Pssm-ID: 468467  Cd Length: 363  Bit Score: 38.66  E-value: 3.15e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1608035124   6 LHIVMALNNTKASEVAEKTGISKSTISKFINGKTDIKLSTLI 47
Cdd:NF038310    1 IKNDLESKGITNRKLAKKIGVSKSTLSKFFNGKGEISFDSLL 42
PRK09726 PRK09726
type II toxin-antitoxin system antitoxin HipB;
4-46 3.78e-03

type II toxin-antitoxin system antitoxin HipB;


Pssm-ID: 182049  Cd Length: 88  Bit Score: 31.87  E-value: 3.78e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 1608035124  4 NNLHIVMALNNTKASEVAEKTGISKSTISKFINGKTDIKLSTL 46
Cdd:PRK09726  15 NAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTF 57
 
Name Accession Description Interval E-value
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
1-53 3.06e-10

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 49.37  E-value: 3.06e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 1608035124  1 MVKNNLHIVMALNNTKASEVAEKTGISKSTISKFINGKTD-IKLSTLISLCIFF 53
Cdd:COG3655    1 MIYVKLDELLAERGMTKKELAEATGISRATLSRLKNGKAKaVRLDTLEKICKAL 54
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
18-53 3.71e-09

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 46.36  E-value: 3.71e-09
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1608035124  18 SEVAEKTGISKSTISKFINGKTDIKLSTLISLCIFF 53
Cdd:smart00530 14 EELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKAL 49
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 18-53 8.52e-09

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: 45.62  E-value: 8.52e-09
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 1608035124 18 SEVAEKTGISKSTISKFINGKTDIKLSTLISLCIFF 53
Cdd:cd00093   16 EELAEKLGVSRSTISRIENGKRNPSLETLEKLAKAL 51
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
18-53 4.58e-08

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 44.22  E-value: 4.58e-08
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 1608035124 18 SEVAEKTGISKSTISKFINGKTDIKLSTLISLCIFF 53
Cdd:COG1396   24 EELAERLGVSRSTISRIERGRRNPSLETLLKLAKAL 59
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 5-53 2.83e-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: 41.76  E-value: 2.83e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 1608035124  5 NLHIVMALNNTKASEVAEKTGISKSTISKFINGKTD-IKLSTLISLCIFF 53
Cdd:pfam13443  1 KLRKLMADRGISKSDLARATGISRATLSRLRKGKPKrVSLDTLDKICDAL 50
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 12-53 3.06e-07

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: 41.76  E-value: 3.06e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 1608035124 12 LNNTKASEVAEKTGISKSTISKFINGKTDIKLSTLISLCIFF 53
Cdd:pfam01381  7 ELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEAL 48
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-53 1.42e-06

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 40.22  E-value: 1.42e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 1608035124  1 MVKNNLHIVMALNNTKASEVAEKTGISKSTISKFINGKTDIKLSTLISLCIFF 53
Cdd:COG1476    4 KLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARAL 56
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 6-53 4.00e-06

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 39.41  E-value: 4.00e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 1608035124  6 LHIVMALNNTKASEVAEKTGISKSTISKFINGKTDIKLSTLISLCIFF 53
Cdd:COG3093   14 REEFLEPLGLSQTELAKALGVSRQRISEILNGKRAITADTALRLARAF 61
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 19-50 8.29e-06

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: 38.85  E-value: 8.29e-06
                         10        20        30
                 ....*....|....*....|....*....|..
gi 1608035124 19 EVAEKTGISKSTISKFINGKTDIKLSTLISLC 50
Cdd:COG3620   35 PVAELVGVSQSDILRIESGKRDPTVSTLEKIA 66
lysogeny_AimR NF038310
AimR family lysis-lysogeny pheromone receptor; The founding member of this family, AimR ...
 6-47 3.15e-05

AimR family lysis-lysogeny pheromone receptor; The founding member of this family, AimR (arbitrium receptor), is a DNA-binding phage regulatory protein that acts as a receptor for a 6-amino acid signaling peptide cleaved from the C-terminus of AimP. AimR controls expression of AimX, the third member of the quorum sensing-like arbitrium system and an inhibitor of phage lysogeny.


Pssm-ID: 468467  Cd Length: 363  Bit Score: 38.66  E-value: 3.15e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1608035124   6 LHIVMALNNTKASEVAEKTGISKSTISKFINGKTDIKLSTLI 47
Cdd:NF038310    1 IKNDLESKGITNRKLAKKIGVSKSTLSKFFNGKGEISFDSLL 42
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 19-53 5.39e-05

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: 36.11  E-value: 5.39e-05
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 1608035124 19 EVAEKTGISKSTISKFINGKTDIKLSTLISLCIFF 53
Cdd:pfam12844 17 ELAERLGISRSQLSAIENGKSVPPAETLYKIAELL 51
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 19-50 6.86e-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: 33.37  E-value: 6.86e-04
                         10        20        30
                 ....*....|....*....|....*....|..
gi 1608035124 19 EVAEKTGISKSTISKFINGKTDIKLSTLISLC 50
Cdd:COG1813   30 ELAEKLGVSESTIRRIERGEATPSLDTLRKLE 61
HTH_LACI smart00354
helix_turn _helix lactose operon repressor;
19-45 9.80e-04

helix_turn _helix lactose operon repressor;


Pssm-ID: 197675 [Multi-domain]  Cd Length: 70  Bit Score: 32.94  E-value: 9.80e-04
                          10        20
                  ....*....|....*....|....*..
gi 1608035124  19 EVAEKTGISKSTISKFINGKTDIKLST 45
Cdd:smart00354  5 DVARLAGVSKATVSRVLNGKGRVSEET 31
PurR COG1609
DNA-binding transcriptional regulator, LacI/PurR family [Transcription];
19-45 2.39e-03

DNA-binding transcriptional regulator, LacI/PurR family [Transcription];


Pssm-ID: 441217 [Multi-domain]  Cd Length: 335  Bit Score: 33.25  E-value: 2.39e-03
                          10        20
                  ....*....|....*....|....*..
gi 1608035124  19 EVAEKTGISKSTISKFINGKTDIKLST 45
Cdd:COG1609     8 DVARLAGVSVATVSRVLNGPPRVSEET 34
PRK09726 PRK09726
type II toxin-antitoxin system antitoxin HipB;
4-46 3.78e-03

type II toxin-antitoxin system antitoxin HipB;


Pssm-ID: 182049  Cd Length: 88  Bit Score: 31.87  E-value: 3.78e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 1608035124  4 NNLHIVMALNNTKASEVAEKTGISKSTISKFINGKTDIKLSTL 46
Cdd:PRK09726  15 NAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTF 57
 
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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