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Conserved domains on  [gi|554766148|ref|WP_023190988|]
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helix-turn-helix domain-containing protein [Lactobacillus helveticus]

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];
1-63 2.90e-12

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 61.17  E-value: 2.90e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 554766148   1 MTIGELLKEERIKKGLTQKQFADSI-VSVSYYSKVEKNEHRITAEDLITILEHNNIPLCSFFKE 63
Cdd:COG1396    6 KALGERLRELRKARGLTQEELAERLgVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGG 69
RGG_Cterm super family cl11770
transcriptional activator, Rgg/GadR/MutR family, C-terminal domain; This model describes the ...
 68-280 5.37e-10

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: 58.05  E-value: 5.37e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 554766148   68 SNFQHEYKIDLEAKVMDAYYHSDKILLEKIIQDLEKSSSTDKTDDILIVKGWLESLKEDEEEPDIEVrNALKDRVFNIPD 147
Cdd:TIGR01716   4 NNYKESEKESFGEKIVEAFYSNDIVGLKSLLSKISETKETYNRLNKAVIKARLHTLDHSYILSEEEV-EFLTDYLFNIEE 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 554766148  148 LNKEKLTLFCNFMDFYDLDSNVMIARKAINKF-ISSNETEIQEVLLAMLANLLCLSIKEDNYNYVEYLVTSSEKLPLKPQ 226
Cdd:TIGR01716  83 WTYYELYLFGNTMSILNSEDLEFLGKELLERLkRYRELNRYRRRVIQLLLNIAVLLIEKNEFSYAQYFLEKLEKILDPED 162

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 554766148  227 FFFYKDMICFYKYLSSYHFNHNKDDLNTCLTIISNVKLAGM----SEYGSELEKFLNN 280
Cdd:TIGR01716 163 DLYERILFNFLKGIILYKEGQKESGEEKIEQAIEIFDELGYptlaAYYQKLLEKFVKK 220
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-63 2.90e-12

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 61.17  E-value: 2.90e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 554766148   1 MTIGELLKEERIKKGLTQKQFADSI-VSVSYYSKVEKNEHRITAEDLITILEHNNIPLCSFFKE 63
Cdd:COG1396    6 KALGERLRELRKARGLTQEELAERLgVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGG 69
RGG_Cterm TIGR01716
transcriptional activator, Rgg/GadR/MutR family, C-terminal domain; This model describes the ...
 68-280 5.37e-10

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: 58.05  E-value: 5.37e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 554766148   68 SNFQHEYKIDLEAKVMDAYYHSDKILLEKIIQDLEKSSSTDKTDDILIVKGWLESLKEDEEEPDIEVrNALKDRVFNIPD 147
Cdd:TIGR01716   4 NNYKESEKESFGEKIVEAFYSNDIVGLKSLLSKISETKETYNRLNKAVIKARLHTLDHSYILSEEEV-EFLTDYLFNIEE 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 554766148  148 LNKEKLTLFCNFMDFYDLDSNVMIARKAINKF-ISSNETEIQEVLLAMLANLLCLSIKEDNYNYVEYLVTSSEKLPLKPQ 226
Cdd:TIGR01716  83 WTYYELYLFGNTMSILNSEDLEFLGKELLERLkRYRELNRYRRRVIQLLLNIAVLLIEKNEFSYAQYFLEKLEKILDPED 162

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 554766148  227 FFFYKDMICFYKYLSSYHFNHNKDDLNTCLTIISNVKLAGM----SEYGSELEKFLNN 280
Cdd:TIGR01716 163 DLYERILFNFLKGIILYKEGQKESGEEKIEQAIEIFDELGYptlaAYYQKLLEKFVKK 220
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 4-57 1.34e-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: 52.94  E-value: 1.34e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 554766148   4 GELLKEERIKKGLTQKQFADSI-VSVSYYSKVEKNEHRITAEDLITILEHNNIPL 57
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLgVSRSTISRIENGKRNPSLETLEKLAKALGVSL 55
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 7-57 9.23e-09

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: 50.62  E-value: 9.23e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 554766148    7 LKEERIKKGLTQKQFADSI-VSVSYYSKVEKNEHRITAEDLITILEHNNIPL 57
Cdd:pfam01381   1 LKELREELGLSQEELAEKLgVSRSTISKIENGKREPSLETLKKLAEALGVSL 52
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
7-57 1.28e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 50.21  E-value: 1.28e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 554766148     7 LKEERIKKGLTQKQFADSI-VSVSYYSKVEKNEHRITAEDLITILEHNNIPL 57
Cdd:smart00530   2 LKELREEKGLTQEELAEKLgVSRSTLSRIENGKRKPSLETLKKLAKALGVSL 53
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-63 2.90e-12

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 61.17  E-value: 2.90e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 554766148   1 MTIGELLKEERIKKGLTQKQFADSI-VSVSYYSKVEKNEHRITAEDLITILEHNNIPLCSFFKE 63
Cdd:COG1396    6 KALGERLRELRKARGLTQEELAERLgVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGG 69
RGG_Cterm TIGR01716
transcriptional activator, Rgg/GadR/MutR family, C-terminal domain; This model describes the ...
 68-280 5.37e-10

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: 58.05  E-value: 5.37e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 554766148   68 SNFQHEYKIDLEAKVMDAYYHSDKILLEKIIQDLEKSSSTDKTDDILIVKGWLESLKEDEEEPDIEVrNALKDRVFNIPD 147
Cdd:TIGR01716   4 NNYKESEKESFGEKIVEAFYSNDIVGLKSLLSKISETKETYNRLNKAVIKARLHTLDHSYILSEEEV-EFLTDYLFNIEE 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 554766148  148 LNKEKLTLFCNFMDFYDLDSNVMIARKAINKF-ISSNETEIQEVLLAMLANLLCLSIKEDNYNYVEYLVTSSEKLPLKPQ 226
Cdd:TIGR01716  83 WTYYELYLFGNTMSILNSEDLEFLGKELLERLkRYRELNRYRRRVIQLLLNIAVLLIEKNEFSYAQYFLEKLEKILDPED 162

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 554766148  227 FFFYKDMICFYKYLSSYHFNHNKDDLNTCLTIISNVKLAGM----SEYGSELEKFLNN 280
Cdd:TIGR01716 163 DLYERILFNFLKGIILYKEGQKESGEEKIEQAIEIFDELGYptlaAYYQKLLEKFVKK 220
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 4-57 1.34e-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: 52.94  E-value: 1.34e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 554766148   4 GELLKEERIKKGLTQKQFADSI-VSVSYYSKVEKNEHRITAEDLITILEHNNIPL 57
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLgVSRSTISRIENGKRNPSLETLEKLAKALGVSL 55
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-63 1.74e-09

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 52.93  E-value: 1.74e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 554766148   1 MTIGELLKEERIKKGLTQKQFADSI-VSVSYYSKVEKNEHRITAEDLITILEHNNIPLCSFFKE 63
Cdd:COG1476    3 KKLGNRLKELRKERGLTQEELAELLgVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSL 66
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 7-57 9.23e-09

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: 50.62  E-value: 9.23e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 554766148    7 LKEERIKKGLTQKQFADSI-VSVSYYSKVEKNEHRITAEDLITILEHNNIPL 57
Cdd:pfam01381   1 LKELREELGLSQEELAEKLgVSRSTISKIENGKREPSLETLKKLAEALGVSL 52
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
7-57 1.28e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 50.21  E-value: 1.28e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 554766148     7 LKEERIKKGLTQKQFADSI-VSVSYYSKVEKNEHRITAEDLITILEHNNIPL 57
Cdd:smart00530   2 LKELREEKGLTQEELAEKLgVSRSTLSRIENGKRKPSLETLKKLAKALGVSL 53
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 2-57 7.35e-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: 48.40  E-value: 7.35e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 554766148   2 TIGELLKEERIKKGLTQKQFADSI-VSVSYYSKVEKNEHRITAEDLITILEHNNIPL 57
Cdd:COG1813   12 DYGERIREAREARGLSQEELAEKLgVSESTIRRIERGEATPSLDTLRKLEKALGISL 68
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 4-51 3.09e-06

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: 43.82  E-value: 3.09e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 554766148    4 GELLKEERIKKGLTQKQFADSI-VSVSYYSKVEKNEHRITAEDLITILE 51
Cdd:pfam12844   1 GERLRKAREERGLTQEELAERLgISRSQLSAIENGKSVPPAETLYKIAE 49
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 1-39 2.18e-05

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: 41.71  E-value: 2.18e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 554766148   1 MTIGELLKEERIKKGLTQKQFADSI-VSVSYYSKVEKNEH 39
Cdd:COG1426    4 ETIGELLRQAREAKGLSLEDVAERTkISVSYLEAIEEGDF 43
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 4-44 3.85e-05

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 41.33  E-value: 3.85e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 554766148   4 GELLKEERIK-KGLTQKQFADSI-VSVSYYSKVEKNEHRITAE 44
Cdd:COG3093   10 GEILREEFLEpLGLSQTELAKALgVSRQRISEILNGKRAITAD 52
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
4-53 1.91e-03

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 36.07  E-value: 1.91e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 554766148   4 GELLKEERIKKGLTQKQFADSI-VSVSYYSKVEKNEHRIT--AEDLITILEHN 53
Cdd:COG2944    8 PEEIRALRERLGLSQAEFAALLgVSVSTVRRWEQGRRKPSgaALKLLRLLEKH 60
 
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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