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Conserved domains on  [gi|494999435|ref|WP_007725451|]
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helix-turn-helix domain-containing protein [Carnobacterium sp. AT7]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 15193268)

helix-turn-helix domain-containing protein such as an XRE (Xenobiotic Response Element) family transcriptional regulator

Gene Ontology:  GO:0003677
PubMed:  10473770|15808743|10556324

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];
1-65 4.63e-07

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 46.91  E-value: 4.63e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 494999435   1 MTHIRQNFGVDFKKIRENKSYTQQYVAQDA-MARSTYTKFEMGNIVPTITKYFQILNNLDMTHEEF 65
Cdd:COG1396    1 MSTLKKALGERLRELRKARGLTQEELAERLgVSRSTISRIERGRRNPSLETLLKLAKALGVSLDEL 66
RGG_Cterm super family cl11770
transcriptional activator, Rgg/GadR/MutR family, C-terminal domain; This model describes the ...
 67-283 5.49e-04

transcriptional activator, Rgg/GadR/MutR family, C-terminal domain; This model describes the whole, except for a 60 residue N-terminal helix-turn-helix DNA-binding domain (pfam01381) of the family of proteins related to the transcriptional regulator Rgg, also called RopB. Rgg is required for secretion of several proteins, including a cysteine proteinase associated with virulence. GadR is a positive regulator of a glutamate-dependent acid resistance mechanism. MutR is a transcriptional activator for mutacin biosynthesis genes in Streptococcus mutans. This family appears restricted to the low-GC Gram-positive bacteria, including at least eight members in Lactococcus lactis. [Regulatory functions, DNA interactions]


The actual alignment was detected with superfamily member TIGR01716:

Pssm-ID: 273772  Cd Length: 220  Bit Score: 40.33  E-value: 5.49e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494999435   67 YIHNDYQLKGKDAILYQFRTMAVNTDIS---ILINVRETTKNYLTEHKDNIVQDIFYICNALITLSKtNDLTQAASYAEK 143
Cdd:TIGR01716   1 YILNNYKESEKESFGEKIVEAFYSNDIVglkSLLSKISETKETYNRLNKAVIKARLHTLDHSYILSE-EEVEFLTDYLFN 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494999435  144 VwhrisqlDKWYLTELRLLNNILFFFDFDTSLFISKRALIELEHYSHF--HEATALKMAYsmNLIYLLMENKNYEQALE- 220
Cdd:TIGR01716  80 I-------EEWTYYELYLFGNTMSILNSEDLEFLGKELLERLKRYRELnrYRRRVIQLLL--NIAVLLIEKNEFSYAQYf 150

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 494999435  221 KADSLILLSKEKERYRILGVLYVrKGIILTKLAKNTEAEVWIQKGFNLLEAIEDFPLKKELDK 283
Cdd:TIGR01716 151 LEKLEKILDPEDDLYERILFNFL-KGIILYKEGQKESGEEKIEQAIEIFDELGYPTLAAYYQK 212
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-65 4.63e-07

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 46.91  E-value: 4.63e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 494999435   1 MTHIRQNFGVDFKKIRENKSYTQQYVAQDA-MARSTYTKFEMGNIVPTITKYFQILNNLDMTHEEF 65
Cdd:COG1396    1 MSTLKKALGERLRELRKARGLTQEELAERLgVSRSTISRIERGRRNPSLETLLKLAKALGVSLDEL 66
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 9-65 6.19e-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: 39.84  E-value: 6.19e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 494999435   9 GVDFKKIRENKSYTQQYVAQDA-MARSTYTKFEMGNIVPTITKYFQILNNLDMTHEEF 65
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLgVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
13-65 1.75e-04

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 38.65  E-value: 1.75e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 494999435    13 KKIRENKSYTQQYVAQDA-MARSTYTKFEMGNIVPTITKYFQILNNLDMTHEEF 65
Cdd:smart00530   3 KELREEKGLTQEELAEKLgVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
RGG_Cterm TIGR01716
transcriptional activator, Rgg/GadR/MutR family, C-terminal domain; This model describes the ...
 67-283 5.49e-04

transcriptional activator, Rgg/GadR/MutR family, C-terminal domain; This model describes the whole, except for a 60 residue N-terminal helix-turn-helix DNA-binding domain (pfam01381) of the family of proteins related to the transcriptional regulator Rgg, also called RopB. Rgg is required for secretion of several proteins, including a cysteine proteinase associated with virulence. GadR is a positive regulator of a glutamate-dependent acid resistance mechanism. MutR is a transcriptional activator for mutacin biosynthesis genes in Streptococcus mutans. This family appears restricted to the low-GC Gram-positive bacteria, including at least eight members in Lactococcus lactis. [Regulatory functions, DNA interactions]


Pssm-ID: 273772  Cd Length: 220  Bit Score: 40.33  E-value: 5.49e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494999435   67 YIHNDYQLKGKDAILYQFRTMAVNTDIS---ILINVRETTKNYLTEHKDNIVQDIFYICNALITLSKtNDLTQAASYAEK 143
Cdd:TIGR01716   1 YILNNYKESEKESFGEKIVEAFYSNDIVglkSLLSKISETKETYNRLNKAVIKARLHTLDHSYILSE-EEVEFLTDYLFN 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494999435  144 VwhrisqlDKWYLTELRLLNNILFFFDFDTSLFISKRALIELEHYSHF--HEATALKMAYsmNLIYLLMENKNYEQALE- 220
Cdd:TIGR01716  80 I-------EEWTYYELYLFGNTMSILNSEDLEFLGKELLERLKRYRELnrYRRRVIQLLL--NIAVLLIEKNEFSYAQYf 150

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 494999435  221 KADSLILLSKEKERYRILGVLYVrKGIILTKLAKNTEAEVWIQKGFNLLEAIEDFPLKKELDK 283
Cdd:TIGR01716 151 LEKLEKILDPEDDLYERILFNFL-KGIILYKEGQKESGEEKIEQAIEIFDELGYPTLAAYYQK 212
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 13-65 1.28e-03

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: 36.36  E-value: 1.28e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 494999435   13 KKIRENKSYTQQYVAQDA-MARSTYTKFEMGNIVPTITKYFQILNNLDMTHEEF 65
Cdd:pfam01381   2 KELREELGLSQEELAEKLgVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-65 4.63e-07

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 46.91  E-value: 4.63e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 494999435   1 MTHIRQNFGVDFKKIRENKSYTQQYVAQDA-MARSTYTKFEMGNIVPTITKYFQILNNLDMTHEEF 65
Cdd:COG1396    1 MSTLKKALGERLRELRKARGLTQEELAERLgVSRSTISRIERGRRNPSLETLLKLAKALGVSLDEL 66
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 9-65 6.19e-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: 39.84  E-value: 6.19e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 494999435   9 GVDFKKIRENKSYTQQYVAQDA-MARSTYTKFEMGNIVPTITKYFQILNNLDMTHEEF 65
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLgVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
13-65 1.75e-04

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 38.65  E-value: 1.75e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 494999435    13 KKIRENKSYTQQYVAQDA-MARSTYTKFEMGNIVPTITKYFQILNNLDMTHEEF 65
Cdd:smart00530   3 KELREEKGLTQEELAEKLgVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
RGG_Cterm TIGR01716
transcriptional activator, Rgg/GadR/MutR family, C-terminal domain; This model describes the ...
 67-283 5.49e-04

transcriptional activator, Rgg/GadR/MutR family, C-terminal domain; This model describes the whole, except for a 60 residue N-terminal helix-turn-helix DNA-binding domain (pfam01381) of the family of proteins related to the transcriptional regulator Rgg, also called RopB. Rgg is required for secretion of several proteins, including a cysteine proteinase associated with virulence. GadR is a positive regulator of a glutamate-dependent acid resistance mechanism. MutR is a transcriptional activator for mutacin biosynthesis genes in Streptococcus mutans. This family appears restricted to the low-GC Gram-positive bacteria, including at least eight members in Lactococcus lactis. [Regulatory functions, DNA interactions]


Pssm-ID: 273772  Cd Length: 220  Bit Score: 40.33  E-value: 5.49e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494999435   67 YIHNDYQLKGKDAILYQFRTMAVNTDIS---ILINVRETTKNYLTEHKDNIVQDIFYICNALITLSKtNDLTQAASYAEK 143
Cdd:TIGR01716   1 YILNNYKESEKESFGEKIVEAFYSNDIVglkSLLSKISETKETYNRLNKAVIKARLHTLDHSYILSE-EEVEFLTDYLFN 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494999435  144 VwhrisqlDKWYLTELRLLNNILFFFDFDTSLFISKRALIELEHYSHF--HEATALKMAYsmNLIYLLMENKNYEQALE- 220
Cdd:TIGR01716  80 I-------EEWTYYELYLFGNTMSILNSEDLEFLGKELLERLKRYRELnrYRRRVIQLLL--NIAVLLIEKNEFSYAQYf 150

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 494999435  221 KADSLILLSKEKERYRILGVLYVrKGIILTKLAKNTEAEVWIQKGFNLLEAIEDFPLKKELDK 283
Cdd:TIGR01716 151 LEKLEKILDPEDDLYERILFNFL-KGIILYKEGQKESGEEKIEQAIEIFDELGYPTLAAYYQK 212
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
13-65 1.18e-03

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 36.75  E-value: 1.18e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 494999435  13 KKIRENKSYTQQYVAQDA-MARSTYTKFEMGNIVPTITKYFQILNNLDMTHEEF 65
Cdd:COG1476   10 KELRKERGLTQEELAELLgVSRQTISAIENGKYNPSLELALKIARALGVSLEEL 63
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 13-65 1.28e-03

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: 36.36  E-value: 1.28e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 494999435   13 KKIRENKSYTQQYVAQDA-MARSTYTKFEMGNIVPTITKYFQILNNLDMTHEEF 65
Cdd:pfam01381   2 KELREELGLSQEELAEKLgVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
 
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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