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Conserved domains on  [gi|496266357|ref|WP_008979742|]
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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];
1-64 3.82e-22

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


:

Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 80.28  E-value: 3.82e-22
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 496266357  1 MKNlKIKMARMELDMSQEELAKKVGATRQTIGLIEAGRYNPSIKLCINICIALHKHLDDLFWDE 64
Cdd:COG1476   5 LGN-RLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLE 67
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-64 3.82e-22

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 80.28  E-value: 3.82e-22
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 496266357  1 MKNlKIKMARMELDMSQEELAKKVGATRQTIGLIEAGRYNPSIKLCINICIALHKHLDDLFWDE 64
Cdd:COG1476   5 LGN-RLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLE 67
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
5-60 1.08e-13

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 58.68  E-value: 1.08e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 496266357    5 KIKMARMELDMSQEELAKKVGATRQTIGLIEAGRYNPSIKLCINICIALHKHLDDL 60
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 5-60 3.17e-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: 57.56  E-value: 3.17e-13
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 496266357  5 KIKMARMELDMSQEELAKKVGATRQTIGLIEAGRYNPSIKLCINICIALHKHLDDL 60
Cdd:cd00093   3 RLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 6-60 1.70e-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: 55.62  E-value: 1.70e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 496266357   6 IKMARMELDMSQEELAKKVGATRQTIGLIEAGRYNPSIKLCINICIALHKHLDDL 60
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
PRK04140 PRK04140
transcriptional regulator;
5-61 3.25e-03

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 34.06  E-value: 3.25e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 496266357   5 KIKMARMELDMSQEELAKKVGATRQTIGLIEAGRYNPSIKlcinicIALhkHLDDLF 61
Cdd:PRK04140 130 VLREAREELGLSLGELASELGVSRRTISKYENGGMNASIE------VAI--KLEEIL 178
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-64 3.82e-22

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 80.28  E-value: 3.82e-22
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 496266357  1 MKNlKIKMARMELDMSQEELAKKVGATRQTIGLIEAGRYNPSIKLCINICIALHKHLDDLFWDE 64
Cdd:COG1476   5 LGN-RLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLE 67
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
5-61 6.85e-14

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 60.01  E-value: 6.85e-14
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 496266357  5 KIKMARMELDMSQEELAKKVGATRQTIGLIEAGRYNPSIKLCINICIALHKHLDDLF 61
Cdd:COG1396  11 RLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELL 67
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
5-60 1.08e-13

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 58.68  E-value: 1.08e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 496266357    5 KIKMARMELDMSQEELAKKVGATRQTIGLIEAGRYNPSIKLCINICIALHKHLDDL 60
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 5-60 3.17e-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: 57.56  E-value: 3.17e-13
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 496266357  5 KIKMARMELDMSQEELAKKVGATRQTIGLIEAGRYNPSIKLCINICIALHKHLDDL 60
Cdd:cd00093   3 RLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 6-60 1.70e-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: 55.62  E-value: 1.70e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 496266357   6 IKMARMELDMSQEELAKKVGATRQTIGLIEAGRYNPSIKLCINICIALHKHLDDL 60
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 5-59 3.32e-10

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: 50.32  E-value: 3.32e-10
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 496266357  5 KIKMARMELDMSQEELAKKVGATRQTIGLIEAGRYNPSIKLCINICIALHKHLDD 59
Cdd:COG1813  16 RIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLAE 70
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 6-60 3.92e-10

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: 50.79  E-value: 3.92e-10
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 496266357  6 IKMARMELDMSQEELAKKVGATRQTIGLIEAGRYNPSIKLCINICIALHKHLDDL 60
Cdd:COG3620  22 LRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAV 76
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 6-41 3.41e-04

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: 3.41e-04
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 496266357   6 IKMARMELDMSQEELAKKVGATRQTIGLIEAGRYNP 41
Cdd:pfam13560  6 LRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGR 41
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 5-40 8.26e-04

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: 34.01  E-value: 8.26e-04
                        10        20        30
                ....*....|....*....|....*....|....*.
gi 496266357  5 KIKMARMELDMSQEELAKKVGATRQTIGLIEAGRYN 40
Cdd:COG1426   9 LLRQAREAKGLSLEDVAERTKISVSYLEAIEEGDFD 44
COG1395 COG1395
Predicted transcriptional regulator [Transcription];
5-43 1.44e-03

Predicted transcriptional regulator [Transcription];


Pssm-ID: 441005 [Multi-domain]  Cd Length: 313  Bit Score: 34.81  E-value: 1.44e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 496266357   5 KIKMARMELDMSQEELAKKVGATRQTIGLIEAGRYNPSI 43
Cdd:COG1395  131 KLRELREERGLSLGELASELGVSRRTISKYERGEMDASI 169
HTH_CRP smart00419
helix_turn_helix, cAMP Regulatory protein;
10-38 2.14e-03

helix_turn_helix, cAMP Regulatory protein;


Pssm-ID: 128696 [Multi-domain]  Cd Length: 48  Bit Score: 32.41  E-value: 2.14e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 496266357   10 RMELDMSQEELAKKVGATRQTI----------GLIEAGR 38
Cdd:smart00419  4 RVRLPLTRQEIAELLGLTRETVsrtlkrlekeGLISREG 42
HTH_Crp_2 pfam13545
Crp-like helix-turn-helix domain; This family represents a crp-like helix-turn-helix domain ...
 10-38 2.52e-03

Crp-like helix-turn-helix domain; This family represents a crp-like helix-turn-helix domain that is likely to bind DNA.


Pssm-ID: 463917 [Multi-domain]  Cd Length: 68  Bit Score: 32.81  E-value: 2.52e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 496266357  10 RMELDMSQEELAKKVGATRQTI----------GLIEAGR 38
Cdd:pfam13545 18 RIDLPLTQEDLADLLGTTRETVsrvlselrreGLIERGR 56
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 5-50 2.90e-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: 32.65  E-value: 2.90e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 496266357   5 KIKMARMELDMSQEELAKKVGATRQTIGLIEAGRYNPSIKLCINIC 50
Cdd:pfam12844  3 RLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIA 48
PRK04140 PRK04140
transcriptional regulator;
5-61 3.25e-03

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 34.06  E-value: 3.25e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 496266357   5 KIKMARMELDMSQEELAKKVGATRQTIGLIEAGRYNPSIKlcinicIALhkHLDDLF 61
Cdd:PRK04140 130 VLREAREELGLSLGELASELGVSRRTISKYENGGMNASIE------VAI--KLEEIL 178
PRK08154 PRK08154
anaerobic benzoate catabolism transcriptional regulator; Reviewed
 5-71 3.45e-03

anaerobic benzoate catabolism transcriptional regulator; Reviewed


Pssm-ID: 236167 [Multi-domain]  Cd Length: 309  Bit Score: 33.77  E-value: 3.45e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 496266357   5 KIKMARMELDMSQEELAKKVGATRQTIGLIEAGRYNPSIKLCINICIALHKHLDDLFWDESYDKEEW 71
Cdd:PRK08154  32 RVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCSLADLLGDVDTSSPDW 98
 
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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