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Conserved domains on  [gi|15598252|ref|NP_251746|]
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hypothetical protein PA3056 [Pseudomonas aeruginosa PAO1]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 10054599)

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:  1.10.10.10
Gene Ontology:  GO:0003677
PubMed:  15808743|2644244|8831795
SCOP:  4000362

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 11-61 2.13e-06

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: 42.93  E-value: 2.13e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 15598252  11 GKRLRALRELMGLSRPQFAELVGMTAKRLENIENELQRMHDEDFEKVCGTF 61
Cdd:cd00093   1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKAL 51
 
Name Accession Description Interval E-value
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 11-61 2.13e-06

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: 42.93  E-value: 2.13e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 15598252  11 GKRLRALRELMGLSRPQFAELVGMTAKRLENIENELQRMHDEDFEKVCGTF 61
Cdd:cd00093   1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKAL 51
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-44 8.42e-05

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 39.21  E-value: 8.42e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 15598252   1 MVKNRRLFtaGKRLRALRELMGLSRPQFAELVGMTAKRLENIEN 44
Cdd:COG1396   1 MSTLKKAL--GERLRELRKARGLTQEELAERLGVSRSTISRIER 42
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 11-45 4.55e-04

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: 36.50  E-value: 4.55e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 15598252    11 GKRLRALRELMGLSRPQFAELVGMTAKRLENIENE 45
Cdd:pfam12844   1 GERLRKAREERGLTQEELAERLGISRSQLSAIENG 35
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
13-61 1.18e-03

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 35.19  E-value: 1.18e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 15598252     13 RLRALRELMGLSRPQFAELVGMTAKRLENIENELQRMHDEDFEKVCGTF 61
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKAL 49
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
11-45 1.96e-03

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 37.08  E-value: 1.96e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 15598252   11 GKRLRALRELMGLSRPQFAELVGMTAKRLENIENE 45
Cdd:PRK09943   9 GKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQD 43
 
Name Accession Description Interval E-value
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 11-61 2.13e-06

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: 42.93  E-value: 2.13e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 15598252  11 GKRLRALRELMGLSRPQFAELVGMTAKRLENIENELQRMHDEDFEKVCGTF 61
Cdd:cd00093   1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKAL 51
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-44 8.42e-05

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 39.21  E-value: 8.42e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 15598252   1 MVKNRRLFtaGKRLRALRELMGLSRPQFAELVGMTAKRLENIEN 44
Cdd:COG1396   1 MSTLKKAL--GERLRELRKARGLTQEELAERLGVSRSTISRIER 42
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 11-45 4.55e-04

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: 36.50  E-value: 4.55e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 15598252    11 GKRLRALRELMGLSRPQFAELVGMTAKRLENIENE 45
Cdd:pfam12844   1 GERLRKAREERGLTQEELAERLGISRSQLSAIENG 35
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
11-61 6.47e-04

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 36.36  E-value: 6.47e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 15598252  11 GKRLRALRELMGLSRPQFAELVGMTAKRLENIENELQRMHDEDFEKVCGTF 61
Cdd:COG1476   6 GNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARAL 56
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 11-61 9.95e-04

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: 36.07  E-value: 9.95e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 15598252  11 GKRLRALRELMGLSRPQFAELVGMTAKRLENIENELQRMHDEDFEKVCGTF 61
Cdd:COG1813  14 GERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKAL 64
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
13-61 1.18e-03

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 35.19  E-value: 1.18e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 15598252     13 RLRALRELMGLSRPQFAELVGMTAKRLENIENELQRMHDEDFEKVCGTF 61
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKAL 49
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
11-44 1.34e-03

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 35.29  E-value: 1.34e-03
                        10        20        30
                ....*....|....*....|....*....|....
gi 15598252  11 GKRLRALRELMGLSRPQFAELVGMTAKRLENIEN 44
Cdd:COG2944   8 PEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQ 41
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 9-45 1.90e-03

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: 35.17  E-value: 1.90e-03
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 15598252   9 TAGKRLRALRELMGLSRPQFAELVGMTAKRLENIENE 45
Cdd:COG1426   5 TIGELLRQAREAKGLSLEDVAERTKISVSYLEAIEEG 41
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
11-45 1.96e-03

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 37.08  E-value: 1.96e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 15598252   11 GKRLRALRELMGLSRPQFAELVGMTAKRLENIENE 45
Cdd:PRK09943   9 GKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQD 43
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 11-54 1.99e-03

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: 1.99e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 15598252    11 GKRLRALRELMGLSRPQFAELVGMTAKRLENIENELQRMHDEDF 54
Cdd:pfam13560   3 GARLRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGRPSPAV 46
 
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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