NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|488334246|ref|WP_002403631|]
View 

MULTISPECIES: helix-turn-helix domain-containing protein [Bacteria]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-65 9.70e-07

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 46.14  E-value: 9.70e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488334246   1 MPNVGNTIKKARKELHLQQKDI--YMGImSRASYTKVESDTKEISLKELSIFSNRLGINFFELLNRS 65
Cdd:COG1396    5 KKALGERLRELRKARGLTQEELaeRLGV-SRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGA 70
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-65 9.70e-07

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 46.14  E-value: 9.70e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488334246   1 MPNVGNTIKKARKELHLQQKDI--YMGImSRASYTKVESDTKEISLKELSIFSNRLGINFFELLNRS 65
Cdd:COG1396    5 KKALGERLRELRKARGLTQEELaeRLGV-SRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGA 70
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 8-61 6.22e-06

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: 42.91  E-value: 6.22e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 488334246    8 IKKARKELHLQQKDI--YMGImSRASYTKVESDTKEISLKELSIFSNRLGINFFEL 61
Cdd:pfam01381   1 LKELREELGLSQEELaeKLGV-SRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 5-61 2.60e-05

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: 41.38  E-value: 2.60e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 488334246   5 GNTIKKARKELHLQQKDI--YMGImSRASYTKVESDTKEISLKELSIFSNRLGINFFEL 61
Cdd:cd00093    1 GERLKELRKEKGLTQEELaeKLGV-SRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
8-61 1.03e-04

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 39.42  E-value: 1.03e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 488334246     8 IKKARKELHLQQKDI--YMGImSRASYTKVESDTKEISLKELSIFSNRLGINFFEL 61
Cdd:smart00530   2 LKELREEKGLTQEELaeKLGV-SRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-65 9.70e-07

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 46.14  E-value: 9.70e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488334246   1 MPNVGNTIKKARKELHLQQKDI--YMGImSRASYTKVESDTKEISLKELSIFSNRLGINFFELLNRS 65
Cdd:COG1396    5 KKALGERLRELRKARGLTQEELaeRLGV-SRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGA 70
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 8-61 6.22e-06

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: 42.91  E-value: 6.22e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 488334246    8 IKKARKELHLQQKDI--YMGImSRASYTKVESDTKEISLKELSIFSNRLGINFFEL 61
Cdd:pfam01381   1 LKELREELGLSQEELaeKLGV-SRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 5-61 2.60e-05

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: 41.38  E-value: 2.60e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 488334246   5 GNTIKKARKELHLQQKDI--YMGImSRASYTKVESDTKEISLKELSIFSNRLGINFFEL 61
Cdd:cd00093    1 GERLKELRKEKGLTQEELaeKLGV-SRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
8-61 1.03e-04

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 39.42  E-value: 1.03e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 488334246     8 IKKARKELHLQQKDI--YMGImSRASYTKVESDTKEISLKELSIFSNRLGINFFEL 61
Cdd:smart00530   2 LKELREEKGLTQEELaeKLGV-SRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 2-60 1.96e-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: 39.15  E-value: 1.96e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488334246   2 PNVGNTIKKARKELHLQQKDI--YMGiMSRASYTKVESDTKEISLKELSIFSNRLGINFFE 60
Cdd:COG1813   11 EDYGERIREAREARGLSQEELaeKLG-VSESTIRRIERGEATPSLDTLRKLEKALGISLAE 70
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
3-62 2.97e-04

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 38.68  E-value: 2.97e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488334246   3 NVGNTIKKARKELHLQQKDI--YMGImSRASYTKVESDTKEISLKELSIFSNRLGINFFELL 62
Cdd:COG1476    4 KLGNRLKELRKERGLTQEELaeLLGV-SRQTISAIENGKYNPSLELALKIARALGVSLEELF 64
 
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