NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|489080813|ref|WP_002990747|]
View 

quorum-sensing system transcriptional regulator Rgg2 [Streptococcus pyogenes]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
RGG_Cterm super family cl11770
transcriptional activator, Rgg/GadR/MutR family, C-terminal domain; This model describes the ...
 66-274 7.32e-39

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: 135.86  E-value: 7.32e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489080813   66 HSKTHTHFFTLLSQARKCYAEKNVVKLTKLLKDYAHKDYER-----TMIKAILFSIDSSIAPSQEELTRLTDYLFKVEQW 140
Cdd:TIGR01716   4 NNYKESEKESFGEKIVEAFYSNDIVGLKSLLSKISETKETYnrlnkAVIKARLHTLDHSYILSEEEVEFLTDYLFNIEEW 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489080813  141 GYYEIILLGNCSRFMNYNTLFLLTKEMVASFAYSEQNKTNKMLVTQLSINCLIISIDHSCFEHSRYLINKIDLLLRDELN 220
Cdd:TIGR01716  84 TYYELYLFGNTMSILNSEDLEFLGKELLERLKRYRELNRYRRRVIQLLLNIAVLLIEKNEFSYAQYFLEKLEKILDPEDD 163

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 489080813  221 FYEKTVFLYVHGYYKLKQEE-MSGEEDMRQALQIFKYLGEDSLYYSYKEHYRQIV 274
Cdd:TIGR01716 164 LYERILFNFLKGIILYKEGQkESGEEKIEQAIEIFDELGYPTLAAYYQKLLEKFV 218
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-72 5.51e-12

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 60.40  E-value: 5.51e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489080813   1 MEKELGKTLRRLRKGKQVSISFLADE-YLSKSQISRFERGESEITCSRLLNLLDKLNITIDEFVSAHSKTHTH 72
Cdd:COG1396    4 LKKALGERLRELRKARGLTQEELAERlGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPE 76
 
Name Accession Description Interval E-value
RGG_Cterm TIGR01716
transcriptional activator, Rgg/GadR/MutR family, C-terminal domain; This model describes the ...
 66-274 7.32e-39

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: 135.86  E-value: 7.32e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489080813   66 HSKTHTHFFTLLSQARKCYAEKNVVKLTKLLKDYAHKDYER-----TMIKAILFSIDSSIAPSQEELTRLTDYLFKVEQW 140
Cdd:TIGR01716   4 NNYKESEKESFGEKIVEAFYSNDIVGLKSLLSKISETKETYnrlnkAVIKARLHTLDHSYILSEEEVEFLTDYLFNIEEW 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489080813  141 GYYEIILLGNCSRFMNYNTLFLLTKEMVASFAYSEQNKTNKMLVTQLSINCLIISIDHSCFEHSRYLINKIDLLLRDELN 220
Cdd:TIGR01716  84 TYYELYLFGNTMSILNSEDLEFLGKELLERLKRYRELNRYRRRVIQLLLNIAVLLIEKNEFSYAQYFLEKLEKILDPEDD 163

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 489080813  221 FYEKTVFLYVHGYYKLKQEE-MSGEEDMRQALQIFKYLGEDSLYYSYKEHYRQIV 274
Cdd:TIGR01716 164 LYERILFNFLKGIILYKEGQkESGEEKIEQAIEIFDELGYPTLAAYYQKLLEKFV 218
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-72 5.51e-12

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 60.40  E-value: 5.51e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489080813   1 MEKELGKTLRRLRKGKQVSISFLADE-YLSKSQISRFERGESEITCSRLLNLLDKLNITIDEFVSAHSKTHTH 72
Cdd:COG1396    4 LKKALGERLRELRKARGLTQEELAERlGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPE 76
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 6-62 1.74e-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: 49.86  E-value: 1.74e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 489080813   6 GKTLRRLRKGKQVSISFLADE-YLSKSQISRFERGESEITCSRLLNLLDKLNITIDEF 62
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKlGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 9-62 1.49e-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: 41.76  E-value: 1.49e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 489080813    9 LRRLRKGKQVSISFLADEY-LSKSQISRFERGESEITCSRLLNLLDKLNITIDEF 62
Cdd:pfam01381   1 LKELREELGLSQEELAEKLgVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
9-62 5.62e-05

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 40.19  E-value: 5.62e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 489080813     9 LRRLRKGKQVSISFLADE-YLSKSQISRFERGESEITCSRLLNLLDKLNITIDEF 62
Cdd:smart00530   2 LKELREEKGLTQEELAEKlGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
 
Name Accession Description Interval E-value
RGG_Cterm TIGR01716
transcriptional activator, Rgg/GadR/MutR family, C-terminal domain; This model describes the ...
 66-274 7.32e-39

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: 135.86  E-value: 7.32e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489080813   66 HSKTHTHFFTLLSQARKCYAEKNVVKLTKLLKDYAHKDYER-----TMIKAILFSIDSSIAPSQEELTRLTDYLFKVEQW 140
Cdd:TIGR01716   4 NNYKESEKESFGEKIVEAFYSNDIVGLKSLLSKISETKETYnrlnkAVIKARLHTLDHSYILSEEEVEFLTDYLFNIEEW 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489080813  141 GYYEIILLGNCSRFMNYNTLFLLTKEMVASFAYSEQNKTNKMLVTQLSINCLIISIDHSCFEHSRYLINKIDLLLRDELN 220
Cdd:TIGR01716  84 TYYELYLFGNTMSILNSEDLEFLGKELLERLKRYRELNRYRRRVIQLLLNIAVLLIEKNEFSYAQYFLEKLEKILDPEDD 163

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 489080813  221 FYEKTVFLYVHGYYKLKQEE-MSGEEDMRQALQIFKYLGEDSLYYSYKEHYRQIV 274
Cdd:TIGR01716 164 LYERILFNFLKGIILYKEGQkESGEEKIEQAIEIFDELGYPTLAAYYQKLLEKFV 218
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-72 5.51e-12

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 60.40  E-value: 5.51e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489080813   1 MEKELGKTLRRLRKGKQVSISFLADE-YLSKSQISRFERGESEITCSRLLNLLDKLNITIDEFVSAHSKTHTH 72
Cdd:COG1396    4 LKKALGERLRELRKARGLTQEELAERlGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPE 76
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 6-62 1.74e-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: 49.86  E-value: 1.74e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 489080813   6 GKTLRRLRKGKQVSISFLADE-YLSKSQISRFERGESEITCSRLLNLLDKLNITIDEF 62
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKlGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-64 2.74e-06

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 44.07  E-value: 2.74e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489080813   1 MEKELGKTLRRLRKGKQVSISFLADE-YLSKSQISRFERGESEITCSRLLNLLDKLNITIDEFVS 64
Cdd:COG1476    1 MKKKLGNRLKELRKERGLTQEELAELlGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFS 65
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 9-62 1.49e-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: 41.76  E-value: 1.49e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 489080813    9 LRRLRKGKQVSISFLADEY-LSKSQISRFERGESEITCSRLLNLLDKLNITIDEF 62
Cdd:pfam01381   1 LKELREELGLSQEELAEKLgVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
9-62 5.62e-05

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 40.19  E-value: 5.62e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 489080813     9 LRRLRKGKQVSISFLADE-YLSKSQISRFERGESEITCSRLLNLLDKLNITIDEF 62
Cdd:smart00530   2 LKELREEKGLTQEELAEKlGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 2-63 1.27e-03

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: 37.31  E-value: 1.27e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489080813   2 EKELGKTLRRLRKGKQVSISFLADEY-LSKSQISRFERGESEITCSRLLNLLDKLNITIDEFV 63
Cdd:COG3620   15 DDTLGEALRLMRKELGLSQLPVAELVgVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVL 77
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 4-61 1.33e-03

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: 36.45  E-value: 1.33e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 489080813   4 ELGKTLRRLRKGKQVSISFLADE-YLSKSQISRFERGESEITCSRLLNLLDKLNITIDE 61
Cdd:COG1813   12 DYGERIREAREARGLSQEELAEKlGVSESTIRRIERGEATPSLDTLRKLEKALGISLAE 70
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 6-62 9.89e-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: 34.19  E-value: 9.89e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 489080813    6 GKTLRRLRKGKQVSISFLADEY-LSKSQISRFERGESEITCSRLLNLLDKLNITIDEF 62
Cdd:pfam12844   1 GERLRKAREERGLTQEELAERLgISRSQLSAIENGKSVPPAETLYKIAELLGVPANWL 58
 
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