NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1822176916|ref|WP_165770250|]
View 

helix-turn-helix transcriptional regulator [Clavibacter sepedonicus]

Protein Classification

helix-turn-helix transcriptional regulator( domain architecture ID 10787697)

helix-turn-helix (HTH) transcriptional regulator containing a XRE (Xenobiotic Response Element) family HTH domain may act as a transcriptional regulator that controls the expression of genes involved in stress response

CATH:  1.10.10.10
Gene Ontology:  GO:0003677
PubMed:  10473770|2644244
SCOP:  4000362

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
12-51 1.36e-08

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


:

Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 46.38  E-value: 1.36e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 1822176916 12 LGEAIKHVRLRRGMTQSDLAEKLGFERFYVRELETGTRPP 51
Cdd:COG1476    5 LGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNP 44
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
12-51 1.36e-08

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 46.38  E-value: 1.36e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 1822176916 12 LGEAIKHVRLRRGMTQSDLAEKLGFERFYVRELETGTRPP 51
Cdd:COG1476    5 LGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNP 44
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 13-51 2.67e-07

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: 42.93  E-value: 2.67e-07
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 1822176916 13 GEAIKHVRLRRGMTQSDLAEKLGFERFYVRELETGTRPP 51
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNP 39
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
16-51 3.67e-06

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 40.19  E-value: 3.67e-06
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1822176916  16 IKHVRLRRGMTQSDLAEKLGFERFYVRELETGTRPP 51
Cdd:smart00530  2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKP 37
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 10-47 2.25e-05

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: 38.02  E-value: 2.25e-05
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 1822176916 10 SDLGEAIKHVRLRRGMTQSDLAEKLGFERFYVRELETG 47
Cdd:TIGR03070  1 KQIGILVRARRKALGLTQADLADLAGVGLRFIRDLENG 38
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 16-51 5.63e-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: 37.13  E-value: 5.63e-05
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 1822176916 16 IKHVRLRRGMTQSDLAEKLGFERFYVRELETGTRPP 51
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREP 36
PRK08154 PRK08154
anaerobic benzoate catabolism transcriptional regulator; Reviewed
 10-48 6.88e-03

anaerobic benzoate catabolism transcriptional regulator; Reviewed


Pssm-ID: 236167 [Multi-domain]  Cd Length: 309  Bit Score: 33.39  E-value: 6.88e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1822176916  10 SDLGEAIKHVRLRRGMTQSDLAEKLGFERFYVRELETGT 48
Cdd:PRK08154   27 AALGERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQ 65
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
12-51 1.36e-08

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 46.38  E-value: 1.36e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 1822176916 12 LGEAIKHVRLRRGMTQSDLAEKLGFERFYVRELETGTRPP 51
Cdd:COG1476    5 LGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNP 44
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
11-51 1.70e-08

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 46.53  E-value: 1.70e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 1822176916 11 DLGEAIKHVRLRRGMTQSDLAEKLGFERFYVRELETGTRPP 51
Cdd:COG1396    7 ALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNP 47
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 1-51 3.15e-08

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: 45.70  E-value: 3.15e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 1822176916  1 MPSHEIRK-YSDLGEAIKHVRLRRGMTQSDLAEKLGFERFYVRELETGTRPP 51
Cdd:COG1813    1 MAKESTGElVEDYGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATP 52
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 13-51 2.67e-07

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: 42.93  E-value: 2.67e-07
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 1822176916 13 GEAIKHVRLRRGMTQSDLAEKLGFERFYVRELETGTRPP 51
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNP 39
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
16-51 3.67e-06

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 40.19  E-value: 3.67e-06
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1822176916  16 IKHVRLRRGMTQSDLAEKLGFERFYVRELETGTRPP 51
Cdd:smart00530  2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKP 37
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 10-47 2.25e-05

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: 38.02  E-value: 2.25e-05
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 1822176916 10 SDLGEAIKHVRLRRGMTQSDLAEKLGFERFYVRELETG 47
Cdd:TIGR03070  1 KQIGILVRARRKALGLTQADLADLAGVGLRFIRDLENG 38
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 16-51 5.63e-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: 37.13  E-value: 5.63e-05
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 1822176916 16 IKHVRLRRGMTQSDLAEKLGFERFYVRELETGTRPP 51
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREP 36
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 5-51 1.26e-04

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: 36.92  E-value: 1.26e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 1822176916  5 EIRKYSDLGEAIKHVRLRRGMTQSDLAEKLGFERFYVRELETGTRPP 51
Cdd:COG3620   11 TVSPDDTLGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDP 57
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 11-51 1.43e-04

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: 35.97  E-value: 1.43e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 1822176916 11 DLGEAIKHVRLRRGMTQSDLAEKLGFERFYVRELETGTRPP 51
Cdd:pfam13560  1 ELGARLRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGR 41
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 12-47 2.79e-04

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: 35.55  E-value: 2.79e-04
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 1822176916 12 LGEAIKHVRLRRGMTQSDLAEKLGFERFYVRELETG 47
Cdd:COG1426    6 IGELLRQAREAKGLSLEDVAERTKISVSYLEAIEEG 41
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 7-50 1.49e-03

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 34.01  E-value: 1.49e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 1822176916  7 RKYSDLGEAIKHVRLR-RGMTQSDLAEKLGFERFYVRELETGTRP 50
Cdd:COG3093    4 RNPIHPGEILREEFLEpLGLSQTELAKALGVSRQRISEILNGKRA 48
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 13-51 4.48e-03

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: 32.26  E-value: 4.48e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 1822176916 13 GEAIKHVRLRRGMTQSDLAEKLGFERFYVRELETGTRPP 51
Cdd:pfam12844  1 GERLRKAREERGLTQEELAERLGISRSQLSAIENGKSVP 39
PRK08154 PRK08154
anaerobic benzoate catabolism transcriptional regulator; Reviewed
 10-48 6.88e-03

anaerobic benzoate catabolism transcriptional regulator; Reviewed


Pssm-ID: 236167 [Multi-domain]  Cd Length: 309  Bit Score: 33.39  E-value: 6.88e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1822176916  10 SDLGEAIKHVRLRRGMTQSDLAEKLGFERFYVRELETGT 48
Cdd:PRK08154   27 AALGERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQ 65
 
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