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Conserved domains on  [gi|495966438|ref|WP_008691017|]
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helix-turn-helix transcriptional regulator [Longicatena caecimuris]

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];
1-66 2.71e-18

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


:

Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 72.96  E-value: 2.71e-18
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 495966438   1 MKIGVKLKEARLQAGLTQENVAEEIQVTRQTISNWETEKSFPDIVSVIKLSTLYNISLDKLLKGDE 66
Cdd:COG1476    3 KKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-66 2.71e-18

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 72.96  E-value: 2.71e-18
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 495966438   1 MKIGVKLKEARLQAGLTQENVAEEIQVTRQTISNWETEKSFPDIVSVIKLSTLYNISLDKLLKGDE 66
Cdd:COG1476    3 KKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 4-61 9.46e-13

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: 58.72  E-value: 9.46e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 495966438   4 GVKLKEARLQAGLTQENVAEEIQVTRQTISNWETEKSFPDIVSVIKLSTLYNISLDKL 61
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
6-61 1.69e-12

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 57.91  E-value: 1.69e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 495966438     6 KLKEARLQAGLTQENVAEEIQVTRQTISNWETEKSFPDIVSVIKLSTLYNISLDKL 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 2.01e-11

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: 55.24  E-value: 2.01e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 495966438    7 LKEARLQAGLTQENVAEEIQVTRQTISNWETEKSFPDIVSVIKLSTLYNISLDKL 61
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
VC1465_fam NF040522
VC1465 family Xer recombination activation factor;
7-40 1.15e-05

VC1465 family Xer recombination activation factor;


Pssm-ID: 439737 [Multi-domain]  Cd Length: 111  Bit Score: 41.66  E-value: 1.15e-05
                         10        20        30
                 ....*....|....*....|....*....|....
gi 495966438   7 LKEARLQAGLTQENVAEEIQVTRQTISNWETEKS 40
Cdd:NF040522   1 IKETREKAGLTRQQAAEMLRVSLRTVQNWETGKV 34
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
4-67 5.13e-05

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 40.93  E-value: 5.13e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 495966438   4 GVKLKEARLQAGLTQENVAEEIQVTRQTISNWETEKSFPDIVSVIKLSTLYNISLDKLLKGDEE 67
Cdd:PRK09943   9 GKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFFSEPEK 72
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-66 2.71e-18

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 72.96  E-value: 2.71e-18
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 495966438   1 MKIGVKLKEARLQAGLTQENVAEEIQVTRQTISNWETEKSFPDIVSVIKLSTLYNISLDKLLKGDE 66
Cdd:COG1476    3 KKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-71 5.40e-18

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 72.72  E-value: 5.40e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 495966438   1 MKIGVKLKEARLQAGLTQENVAEEIQVTRQTISNWETEKSFPDIVSVIKLSTLYNISLDKLLKGDEEMIEH 71
Cdd:COG1396    6 KALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPE 76
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 4-61 9.46e-13

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: 58.72  E-value: 9.46e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 495966438   4 GVKLKEARLQAGLTQENVAEEIQVTRQTISNWETEKSFPDIVSVIKLSTLYNISLDKL 61
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
6-61 1.69e-12

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 57.91  E-value: 1.69e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 495966438     6 KLKEARLQAGLTQENVAEEIQVTRQTISNWETEKSFPDIVSVIKLSTLYNISLDKL 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 2.01e-11

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: 55.24  E-value: 2.01e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 495966438    7 LKEARLQAGLTQENVAEEIQVTRQTISNWETEKSFPDIVSVIKLSTLYNISLDKL 61
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 3-59 6.42e-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: 54.17  E-value: 6.42e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 495966438   3 IGVKLKEARLQAGLTQENVAEEIQVTRQTISNWETEKSFPDIVSVIKLSTLYNISLD 59
Cdd:COG1813   13 YGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLA 69
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 4-64 2.23e-09

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: 50.36  E-value: 2.23e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 495966438    4 GVKLKEARLQAGLTQENVAEEIQVTRQTISNWETEKSFPDIVSVIKLSTLYNISLDKLLKG 64
Cdd:pfam12844   1 GERLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLLQG 61
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 3-72 4.09e-08

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: 46.75  E-value: 4.09e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495966438    3 IGVKLKEARLQAGLTQENVAEEIQVTRQTISNWETEKsfpdiVSVIKLSTLynISLDKLLKGDEEMIEHL 72
Cdd:pfam13560   2 LGARLRRLRERAGLSQEALARRLGVSRSTLSRLETGR-----RGRPSPAVV--ERLARALGVDGAERAEL 64
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
4-43 1.59e-06

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 42.61  E-value: 1.59e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 495966438   4 GVKLKEARLQAGLTQENVAEEIQVTRQTISNWETEKSFPD 43
Cdd:COG2944    8 PEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPS 47
VC1465_fam NF040522
VC1465 family Xer recombination activation factor;
7-40 1.15e-05

VC1465 family Xer recombination activation factor;


Pssm-ID: 439737 [Multi-domain]  Cd Length: 111  Bit Score: 41.66  E-value: 1.15e-05
                         10        20        30
                 ....*....|....*....|....*....|....
gi 495966438   7 LKEARLQAGLTQENVAEEIQVTRQTISNWETEKS 40
Cdd:NF040522   1 IKETREKAGLTRQQAAEMLRVSLRTVQNWETGKV 34
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 1-72 1.54e-05

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: 40.77  E-value: 1.54e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 495966438   1 MKIGVKLKEARLQAGLTQENVAEEIQVTRQTISNWETEKSFPDIVSVIKLSTLYNISLDKLLKGDEEMIEHL 72
Cdd:COG3620   16 DTLGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVLVVDDGKLVGI 87
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 1-39 3.06e-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: 39.40  E-value: 3.06e-05
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 495966438   1 MKIGVKLKEARLQAGLTQENVAEEIQVTRQTISNWETEK 39
Cdd:COG1426    4 ETIGELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGD 42
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
4-67 5.13e-05

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 40.93  E-value: 5.13e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 495966438   4 GVKLKEARLQAGLTQENVAEEIQVTRQTISNWETEKSFPDIVSVIKLSTLYNISLDKLLKGDEE 67
Cdd:PRK09943   9 GKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFFSEPEK 72
PRK10856 PRK10856
cytoskeleton protein RodZ;
4-46 1.97e-04

cytoskeleton protein RodZ;


Pssm-ID: 236776 [Multi-domain]  Cd Length: 331  Bit Score: 39.62  E-value: 1.97e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 495966438   4 GVKLKEARLQAGLTQENVAEEIQVTRQTISNWETEKSFPDIVS 46
Cdd:PRK10856  16 GERLRQAREQLGLTQQAVAERLCLKVSTVRDIEEDKAPADLAS 58
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 3-67 3.01e-04

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 38.30  E-value: 3.01e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 495966438   3 IGVKLKEARLQAGLTQENVAEEIQVTRQTISNWETEKSFPDIVSVIKLSTLYNISLDKLLKGDEE 67
Cdd:PRK09706   6 LGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCSPTWLLFGDED 70
Phage_CI_repr pfam07022
Bacteriophage CI repressor helix-turn-helix domain; This family consists of several phage CI ...
 17-68 1.79e-03

Bacteriophage CI repressor helix-turn-helix domain; This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic.


Pssm-ID: 311152  Cd Length: 65  Bit Score: 34.61  E-value: 1.79e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 495966438   17 TQENVAEEIQVTRQTISNWETEKSFP-DIVSVIKLSTlyNISLDKLLKGDEEM 68
Cdd:pfam07022  14 SRQELADHLGVSKSTLSTWYTRDSFPaELVVRCALET--GVSLEWLATGDGEL 64
PHA01976 PHA01976
helix-turn-helix protein
 1-67 6.16e-03

helix-turn-helix protein


Pssm-ID: 177330 [Multi-domain]  Cd Length: 67  Bit Score: 33.39  E-value: 6.16e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 495966438   1 MKIGVKLKEARLQAGLTQENVAEEIQVTRQTISNWETEKSFPDIVSVIKLSTLYNISLDKLLKGDEE 67
Cdd:PHA01976   1 MSFAIQLIKARNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTLDWLCGRCGE 67
 
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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