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Conserved domains on  [gi|500943100|ref|WP_012027880|]
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helix-turn-helix domain-containing protein [Streptococcus suis]

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
RGG_Cterm super family cl11770
transcriptional activator, Rgg/GadR/MutR family, C-terminal domain; This model describes the ...
 63-285 3.05e-37

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: 131.62  E-value: 3.05e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500943100   63 YASQDFKKDELTRILEQLKQSIYIRDVVTIKKILSEQlakaeRDSRREFHRLNAILIAYKLRNLDKTIVVSKEDTAFLTD 142
Cdd:TIGR01716   1 YILNNYKESEKESFGEKIVEAFYSNDIVGLKSLLSKI-----SETKETYNRLNKAVIKARLHTLDHSYILSEEEVEFLTD 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500943100  143 YLFRVENWSYYEILLFANTIDKLGHQTMMLFCRELIHRTQFYREMKQHRLVVSQVLLSAYLVSVQTKELVDAIFLEKTIE 222
Cdd:TIGR01716  76 YLFNIEEWTYYELYLFGNTMSILNSEDLEFLGKELLERLKRYRELNRYRRRVIQLLLNIAVLLIEKNEFSYAQYFLEKLE 155

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 500943100  223 GLLFDETEIFERILFKFGKAFYDYQNTGTSNAILEMRKCIGLLRAVDSQNIADWYESILEKIL 285
Cdd:TIGR01716 156 KILDPEDDLYERILFNFLKGIILYKEGQKESGEEKIEQAIEIFDELGYPTLAAYYQKLLEKFV 218
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
4-67 6.73e-10

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 54.62  E-value: 6.73e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 500943100   4 FGKTLKFIREGKGKSLAEVA-KGHISTSQLSRFENGESDITVSKLFGVLAEMNVDVDEFVYASQD 67
Cdd:COG1396    8 LGERLRELRKARGLTQEELAeRLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADE 72
 
Name Accession Description Interval E-value
RGG_Cterm TIGR01716
transcriptional activator, Rgg/GadR/MutR family, C-terminal domain; This model describes the ...
 63-285 3.05e-37

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: 131.62  E-value: 3.05e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500943100   63 YASQDFKKDELTRILEQLKQSIYIRDVVTIKKILSEQlakaeRDSRREFHRLNAILIAYKLRNLDKTIVVSKEDTAFLTD 142
Cdd:TIGR01716   1 YILNNYKESEKESFGEKIVEAFYSNDIVGLKSLLSKI-----SETKETYNRLNKAVIKARLHTLDHSYILSEEEVEFLTD 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500943100  143 YLFRVENWSYYEILLFANTIDKLGHQTMMLFCRELIHRTQFYREMKQHRLVVSQVLLSAYLVSVQTKELVDAIFLEKTIE 222
Cdd:TIGR01716  76 YLFNIEEWTYYELYLFGNTMSILNSEDLEFLGKELLERLKRYRELNRYRRRVIQLLLNIAVLLIEKNEFSYAQYFLEKLE 155

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 500943100  223 GLLFDETEIFERILFKFGKAFYDYQNTGTSNAILEMRKCIGLLRAVDSQNIADWYESILEKIL 285
Cdd:TIGR01716 156 KILDPEDDLYERILFNFLKGIILYKEGQKESGEEKIEQAIEIFDELGYPTLAAYYQKLLEKFV 218
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
4-67 6.73e-10

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 54.62  E-value: 6.73e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 500943100   4 FGKTLKFIREGKGKSLAEVA-KGHISTSQLSRFENGESDITVSKLFGVLAEMNVDVDEFVYASQD 67
Cdd:COG1396    8 LGERLRELRKARGLTQEELAeRLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADE 72
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 5-61 9.71e-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: 50.63  E-value: 9.71e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 500943100   5 GKTLKFIREGKGKSLAEVAKG-HISTSQLSRFENGESDITVSKLFGVLAEMNVDVDEF 61
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKlGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
8-61 3.71e-07

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 46.36  E-value: 3.71e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 500943100     8 LKFIREGKGKSLAEVAKG-HISTSQLSRFENGESDITVSKLFGVLAEMNVDVDEF 61
Cdd:smart00530   2 LKELREEKGLTQEELAEKlGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 8-61 4.46e-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: 43.30  E-value: 4.46e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 500943100    8 LKFIREGKGKSLAEVAK-GHISTSQLSRFENGESDITVSKLFGVLAEMNVDVDEF 61
Cdd:pfam01381   1 LKELREELGLSQEELAEkLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
 
Name Accession Description Interval E-value
RGG_Cterm TIGR01716
transcriptional activator, Rgg/GadR/MutR family, C-terminal domain; This model describes the ...
 63-285 3.05e-37

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: 131.62  E-value: 3.05e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500943100   63 YASQDFKKDELTRILEQLKQSIYIRDVVTIKKILSEQlakaeRDSRREFHRLNAILIAYKLRNLDKTIVVSKEDTAFLTD 142
Cdd:TIGR01716   1 YILNNYKESEKESFGEKIVEAFYSNDIVGLKSLLSKI-----SETKETYNRLNKAVIKARLHTLDHSYILSEEEVEFLTD 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500943100  143 YLFRVENWSYYEILLFANTIDKLGHQTMMLFCRELIHRTQFYREMKQHRLVVSQVLLSAYLVSVQTKELVDAIFLEKTIE 222
Cdd:TIGR01716  76 YLFNIEEWTYYELYLFGNTMSILNSEDLEFLGKELLERLKRYRELNRYRRRVIQLLLNIAVLLIEKNEFSYAQYFLEKLE 155

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 500943100  223 GLLFDETEIFERILFKFGKAFYDYQNTGTSNAILEMRKCIGLLRAVDSQNIADWYESILEKIL 285
Cdd:TIGR01716 156 KILDPEDDLYERILFNFLKGIILYKEGQKESGEEKIEQAIEIFDELGYPTLAAYYQKLLEKFV 218
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
4-67 6.73e-10

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 54.62  E-value: 6.73e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 500943100   4 FGKTLKFIREGKGKSLAEVA-KGHISTSQLSRFENGESDITVSKLFGVLAEMNVDVDEFVYASQD 67
Cdd:COG1396    8 LGERLRELRKARGLTQEELAeRLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADE 72
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 5-61 9.71e-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: 50.63  E-value: 9.71e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 500943100   5 GKTLKFIREGKGKSLAEVAKG-HISTSQLSRFENGESDITVSKLFGVLAEMNVDVDEF 61
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKlGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
8-61 3.71e-07

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 46.36  E-value: 3.71e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 500943100     8 LKFIREGKGKSLAEVAKG-HISTSQLSRFENGESDITVSKLFGVLAEMNVDVDEF 61
Cdd:smart00530   2 LKELREEKGLTQEELAEKlGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 8-61 4.46e-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: 43.30  E-value: 4.46e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 500943100    8 LKFIREGKGKSLAEVAK-GHISTSQLSRFENGESDITVSKLFGVLAEMNVDVDEF 61
Cdd:pfam01381   1 LKELREELGLSQEELAEkLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
4-66 8.80e-05

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 39.83  E-value: 8.80e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 500943100   4 FGKTLKFIREGKGKSLAEVAKG-HISTSQLSRFENGESDITVSKLFGVLAEMNVDVDEFVYASQ 66
Cdd:COG1476    5 LGNRLKELRKERGLTQEELAELlGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 5-61 5.13e-04

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: 37.65  E-value: 5.13e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 500943100    5 GKTLKFIREGKGKSLAEVAK-GHISTSQLSRFENGESDITVSKLFGVLAEMNVDVDEF 61
Cdd:pfam12844   1 GERLRKAREERGLTQEELAErLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWL 58
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 4-41 1.08e-03

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: 36.71  E-value: 1.08e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 500943100   4 FGKTLKFIREGKGKSLAEVAKG-HISTSQLSRFENGESD 41
Cdd:COG1426    6 IGELLRQAREAKGLSLEDVAERtKISVSYLEAIEEGDFD 44
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 4-62 1.39e-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: 1.39e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 500943100   4 FGKTLKFIREGKGKSLAEVAK--GhISTSQLSRFENGESDITVSKLFGVLAEMNVDVDEFV 62
Cdd:COG3620   18 LGEALRLMRKELGLSQLPVAElvG-VSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVL 77
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 4-39 5.74e-03

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: 34.81  E-value: 5.74e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 500943100    4 FGKTLKFIREGKGKSLAEVAKG-HISTSQLSRFENGE 39
Cdd:pfam13560   2 LGARLRRLRERAGLSQEALARRlGVSRSTLSRLETGR 38
 
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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