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Conserved domains on  [gi|1408148944|ref|WP_111524762|]
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helix-turn-helix transcriptional regulator [Lachnoanaerobaculum umeaense]

Protein Classification

helix-turn-helix transcriptional regulator( domain architecture ID 10787697)

helix-turn-helix (HTH) transcriptional regulator containing a XRE (Xenobiotic Response Element) family HTH domain may act as a transcriptional regulator that controls the expression of genes involved in stress response

CATH:  1.10.10.10
Gene Ontology:  GO:0003677
PubMed:  10473770|2644244
SCOP:  4000362

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-65 2.55e-16

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


:

Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 67.18  E-value: 2.55e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1408148944   1 MSIGSRIKEKRAELNLSRADLADKIGVSASAIANYENEVSVPKIELMYKILSALKCDANYLYQDN 65
Cdd:COG1476     3 KKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLE 67
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-65 2.55e-16

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 67.18  E-value: 2.55e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1408148944   1 MSIGSRIKEKRAELNLSRADLADKIGVSASAIANYENEVSVPKIELMYKILSALKCDANYLYQDN 65
Cdd:COG1476     3 KKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLE 67
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 4-61 2.65e-14

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: 61.80  E-value: 2.65e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1408148944   4 GSRIKEKRAELNLSRADLADKIGVSASAIANYENEVSVPKIELMYKILSALKCDANYL 61
Cdd:cd00093     1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
6-61 1.69e-13

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 59.84  E-value: 1.69e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1408148944    6 RIKEKRAELNLSRADLADKIGVSASAIANYENEVSVPKIELMYKILSALKCDANYL 61
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 7-61 2.25e-12

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: 56.78  E-value: 2.25e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1408148944   7 IKEKRAELNLSRADLADKIGVSASAIANYENEVSVPKIELMYKILSALKCDANYL 61
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 2-61 2.84e-07

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 45.61  E-value: 2.84e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1408148944   2 SIGSRIKEKRAELNLSRADLADKIGVSASAIANYENEVSVPKIELMYKILSALKCDANYL 61
Cdd:PRK09706    5 TLGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCSPTWL 64
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 3-54 3.10e-07

transcriptional regulator, y4mF family; Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems. [Regulatory functions, DNA interactions]


Pssm-ID: 213767 [Multi-domain]  Cd Length: 58  Bit Score: 43.80  E-value: 3.10e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1408148944   3 IGSRIKEKRAELNLSRADLADKIGVSASAIANYENEVSVPKIELMYKILSAL 54
Cdd:TIGR03070   3 IGILVRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDAL 54
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-65 2.55e-16

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 67.18  E-value: 2.55e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1408148944   1 MSIGSRIKEKRAELNLSRADLADKIGVSASAIANYENEVSVPKIELMYKILSALKCDANYLYQDN 65
Cdd:COG1476     3 KKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLE 67
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-64 2.83e-16

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 67.71  E-value: 2.83e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1408148944   1 MSIGSRIKEKRAELNLSRADLADKIGVSASAIANYENEVSVPKIELMYKILSALKCDANYLYQD 64
Cdd:COG1396     6 KALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGG 69
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 4-61 2.65e-14

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: 61.80  E-value: 2.65e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1408148944   4 GSRIKEKRAELNLSRADLADKIGVSASAIANYENEVSVPKIELMYKILSALKCDANYL 61
Cdd:cd00093     1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
6-61 1.69e-13

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 59.84  E-value: 1.69e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1408148944    6 RIKEKRAELNLSRADLADKIGVSASAIANYENEVSVPKIELMYKILSALKCDANYL 61
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 7-61 2.25e-12

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: 56.78  E-value: 2.25e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1408148944   7 IKEKRAELNLSRADLADKIGVSASAIANYENEVSVPKIELMYKILSALKCDANYL 61
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 3-57 4.30e-11

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: 53.79  E-value: 4.30e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1408148944   3 IGSRIKEKRAELNLSRADLADKIGVSASAIANYENEVSVPKIELMYKILSALKCD 57
Cdd:COG1813    13 YGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGIS 67
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 4-63 1.18e-10

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: 52.68  E-value: 1.18e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1408148944   4 GSRIKEKRAELNLSRADLADKIGVSASAIANYENEVSVPKIELMYKILSALKCDANYLYQ 63
Cdd:pfam12844   1 GERLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLLQ 60
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 1-61 3.60e-09

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: 49.63  E-value: 3.60e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1408148944   1 MSIGSRIKEKRAELNLSRADLADKIGVSASAIANYENEVSVPKIELMYKILSALKCDANYL 61
Cdd:COG3620    16 DTLGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAV 76
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 2-61 2.84e-07

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 45.61  E-value: 2.84e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1408148944   2 SIGSRIKEKRAELNLSRADLADKIGVSASAIANYENEVSVPKIELMYKILSALKCDANYL 61
Cdd:PRK09706    5 TLGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCSPTWL 64
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 3-54 3.10e-07

transcriptional regulator, y4mF family; Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems. [Regulatory functions, DNA interactions]


Pssm-ID: 213767 [Multi-domain]  Cd Length: 58  Bit Score: 43.80  E-value: 3.10e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1408148944   3 IGSRIKEKRAELNLSRADLADKIGVSASAIANYENEVSVPKIELMYKILSAL 54
Cdd:TIGR03070   3 IGILVRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDAL 54
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
4-37 4.85e-07

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 43.38  E-value: 4.85e-07
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1408148944   4 GSRIKEKRAELNLSRADLADKIGVSASAIANYEN 37
Cdd:COG2944     8 PEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQ 41
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 1-61 9.71e-06

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: 40.17  E-value: 9.71e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1408148944   1 MSIGSRIKEKRAELNLSRADLADKIGVSASAIANYENE------VSVPKIELMYKILSALKCDANYL 61
Cdd:COG1426     4 ETIGELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGdfdalpGPVYVRGFLRSYARALGLDPEEL 70
COG1395 COG1395
Predicted transcriptional regulator [Transcription];
4-57 1.10e-05

Predicted transcriptional regulator [Transcription];


Pssm-ID: 441005 [Multi-domain]  Cd Length: 313  Bit Score: 42.52  E-value: 1.10e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1408148944   4 GSRIKEKRAELNLSRADLADKIGVSASAIANYENEVSVPKIELMYKILSALKCD 57
Cdd:COG1395   129 GEKLRELREERGLSLGELASELGVSRRTISKYERGEMDASIEVALKLEEILGEP 182
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 3-57 3.89e-05

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: 38.28  E-value: 3.89e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1408148944   3 IGSRIKEKRAELNLSRADLADKIGVSASAIANYEN-EVSVPKIELMYKILSALKCD 57
Cdd:pfam13560   2 LGARLRRLRERAGLSQEALARRLGVSRSTLSRLETgRRGRPSPAVVERLARALGVD 57
PRK09726 PRK09726
type II toxin-antitoxin system antitoxin HipB;
7-54 2.33e-04

type II toxin-antitoxin system antitoxin HipB;


Pssm-ID: 182049  Cd Length: 88  Bit Score: 37.27  E-value: 2.33e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1408148944   7 IKEKRAELNLSRADLADKIGVSASAIANYENEVSVPKIELMYKILSAL 54
Cdd:PRK09726   17 MKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSL 64
PRK04140 PRK04140
transcriptional regulator;
4-45 3.81e-04

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 37.91  E-value: 3.81e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1408148944   4 GSRIKEKRAELNLSRADLADKIGVSASAIANYENEVSVPKIE 45
Cdd:PRK04140  128 GDVLREAREELGLSLGELASELGVSRRTISKYENGGMNASIE 169
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
2-57 1.19e-03

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 34.73  E-value: 1.19e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1408148944   2 SIGSRIKEKRAELNLSRADLADKIGVSASAIANYEN-EVSVPKIELMYKILSALKCD 57
Cdd:COG3655     1 MIYVKLDELLAERGMTKKELAEATGISRATLSRLKNgKAKAVRLDTLEKICKALDCQ 57
PRK13355 PRK13355
bifunctional HTH-domain containing protein/aminotransferase; Provisional
 4-61 1.24e-03

bifunctional HTH-domain containing protein/aminotransferase; Provisional


Pssm-ID: 237361 [Multi-domain]  Cd Length: 517  Bit Score: 36.64  E-value: 1.24e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1408148944   4 GSRIKEKRAELNLSRADLADK-----IGVSASAIANYENEVSVPKIELMYKILSALKCDANYL 61
Cdd:PRK13355    5 AERLKQAMKARGLKQEDLVHAaeargVKLGKSHISQYVSGKTGPRRDVLPFLAAILGVSEDWL 67
COG1709 COG1709
Predicted transcriptional regulator,contains XRE-type HTH domain [Transcription];
2-36 2.66e-03

Predicted transcriptional regulator,contains XRE-type HTH domain [Transcription];


Pssm-ID: 441315  Cd Length: 234  Bit Score: 35.54  E-value: 2.66e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1408148944   2 SIGSRIKEKRAELNLSRADLADKIGVSASAIANYE 36
Cdd:COG1709    22 DPGETLRKWREDFGISQTELARELGVSPSVISDYE 56
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 6-57 3.30e-03

Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to DNA.


Pssm-ID: 433211 [Multi-domain]  Cd Length: 63  Bit Score: 33.28  E-value: 3.30e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1408148944   6 RIKEKRAELNLSRADLADKIGVSASAIANYEN-EVSVPKIELMYKILSALKCD 57
Cdd:pfam13443   1 KLRKLMADRGISKSDLARATGISRATLSRLRKgKPKRVSLDTLDKICDALGCQ 53
 
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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