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Conserved domains on  [gi|119377049|gb|ABL71813|]
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putative transcriptional regulator, XRE family [Paracoccus denitrificans PD1222]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 10582316)

helix-turn-helix (HTH) domain-containing protein with an XRE (Xenobiotic Response Element) family HTH domain, binds DNA and may function as a transcriptional regulator

CATH:  1.10.260.40
Gene Ontology:  GO:0003677
PubMed:  2644244|15808743|8831795|10473770
SCOP:  4000362

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 39-106 3.05e-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: 53.06  E-value: 3.05e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 119377049   39 LRALREGAKVGVREMARRLGISPNSYTHYENPNRfkdpylpMHWAERFADALEPDGVPRDAVLALAGV 106
Cdd:pfam12844   4 LRKAREERGLTQEELAERLGISRSQLSAIENGKS-------VPPAETLYKIAELLGVPANWLLQGEGE 64
 
Name Accession Description Interval E-value
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 39-106 3.05e-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: 53.06  E-value: 3.05e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 119377049   39 LRALREGAKVGVREMARRLGISPNSYTHYENPNRfkdpylpMHWAERFADALEPDGVPRDAVLALAGV 106
Cdd:pfam12844   4 LRKAREERGLTQEELAERLGISRSQLSAIENGKS-------VPPAETLYKIAELLGVPANWLLQGEGE 64
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
39-102 1.51e-04

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 38.44  E-value: 1.51e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 119377049  39 LRALREGAKVGVREMARRLGISPNSYTHYENPNRfkdpYLPMHWAERFADALepdGVPRDAVLA 102
Cdd:COG1396   12 LRELRKARGLTQEELAERLGVSRSTISRIERGRR----NPSLETLLKLAKAL---GVSLDELLG 68
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 38-69 1.66e-04

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: 37.53  E-value: 1.66e-04
                         10        20        30
                 ....*....|....*....|....*....|..
gi 119377049  38 ALRALREGAKVGVREMARRLGISPNSYTHYEN 69
Cdd:cd00093    3 RLKELRKEKGLTQEELAEKLGVSRSTISRIEN 34
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
39-69 1.77e-04

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 37.50  E-value: 1.77e-04
                           10        20        30
                   ....*....|....*....|....*....|.
gi 119377049    39 LRALREGAKVGVREMARRLGISPNSYTHYEN 69
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIEN 32
 
Name Accession Description Interval E-value
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 39-106 3.05e-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: 53.06  E-value: 3.05e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 119377049   39 LRALREGAKVGVREMARRLGISPNSYTHYENPNRfkdpylpMHWAERFADALEPDGVPRDAVLALAGV 106
Cdd:pfam12844   4 LRKAREERGLTQEELAERLGISRSQLSAIENGKS-------VPPAETLYKIAELLGVPANWLLQGEGE 64
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 39-99 4.39e-07

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: 44.83  E-value: 4.39e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 119377049   39 LRALREGAKVGVREMARRLGISPNSYTHYENPnrfKDPYLPMHWAERFADALEPDGVPRDA 99
Cdd:pfam13560   6 LRRLRERAGLSQEALARRLGVSRSTLSRLETG---RRGRPSPAVVERLARALGVDGAERAE 63
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
39-102 1.51e-04

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 38.44  E-value: 1.51e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 119377049  39 LRALREGAKVGVREMARRLGISPNSYTHYENPNRfkdpYLPMHWAERFADALepdGVPRDAVLA 102
Cdd:COG1396   12 LRELRKARGLTQEELAERLGVSRSTISRIERGRR----NPSLETLLKLAKAL---GVSLDELLG 68
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 38-69 1.66e-04

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: 37.53  E-value: 1.66e-04
                         10        20        30
                 ....*....|....*....|....*....|..
gi 119377049  38 ALRALREGAKVGVREMARRLGISPNSYTHYEN 69
Cdd:cd00093    3 RLKELRKEKGLTQEELAEKLGVSRSTISRIEN 34
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
39-69 1.77e-04

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 37.50  E-value: 1.77e-04
                           10        20        30
                   ....*....|....*....|....*....|.
gi 119377049    39 LRALREGAKVGVREMARRLGISPNSYTHYEN 69
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIEN 32
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 39-69 2.06e-03

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: 34.82  E-value: 2.06e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 119377049   39 LRALREGAKVGVREMARRLGISPNSYTHYEN 69
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIEN 31
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 27-93 6.59e-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: 34.23  E-value: 6.59e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 119377049  27 ATSMSDQQVTYALRALREGAKVGVREMARRLGISPNSYTHYENPNRfkDPYLPMhwAERFADALEPD 93
Cdd:COG3620   10 VTVSPDDTLGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKR--DPTVST--LEKIAEALGKE 72
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
38-91 7.88e-03

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 33.28  E-value: 7.88e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 119377049  38 ALRALREGAKVGVREMARRLGISPNSYTHYENpnrfkDPYLP-MHWAERFADALE 91
Cdd:COG1476    8 RLKELRKERGLTQEELAELLGVSRQTISAIEN-----GKYNPsLELALKIARALG 57
 
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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