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Conserved domains on  [gi|15599272|ref|NP_252766|]
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transcriptional regulator [Pseudomonas aeruginosa PAO1]

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 4.68e-27

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


:

Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 92.60  E-value: 4.68e-27
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15599272  1 MRNRVRELRAERGWSQAELAGKLEVSRQTVNAIETGRYDPSLPLAFKLARVFGLAIEAIFDDRE 64
Cdd:COG1476  5 LGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-64 4.68e-27

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 92.60  E-value: 4.68e-27
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15599272  1 MRNRVRELRAERGWSQAELAGKLEVSRQTVNAIETGRYDPSLPLAFKLARVFGLAIEAIFDDRE 64
Cdd:COG1476  5 LGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
4-59 1.98e-16

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 65.62  E-value: 1.98e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 15599272     4 RVRELRAERGWSQAELAGKLEVSRQTVNAIETGRYDPSLPLAFKLARVFGLAIEAI 59
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 3-59 8.07e-16

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: 64.11  E-value: 8.07e-16
                       10        20        30        40        50
               ....*....|....*....|....*....|....*....|....*....|....*..
gi 15599272  3 NRVRELRAERGWSQAELAGKLEVSRQTVNAIETGRYDPSLPLAFKLARVFGLAIEAI 59
Cdd:cd00093  2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 5-59 6.79e-14

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: 59.09  E-value: 6.79e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 15599272    5 VRELRAERGWSQAELAGKLEVSRQTVNAIETGRYDPSLPLAFKLARVFGLAIEAI 59
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
PRK04140 PRK04140
transcriptional regulator;
3-56 7.35e-07

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 44.08  E-value: 7.35e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 15599272    3 NRVRELRAERGWSQAELAGKLEVSRQTVNAIETGRYDPSLPLAFKLARVFGLAI 56
Cdd:PRK04140 129 DVLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDVPL 182
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 13-53 3.23e-05

addiction module antidote protein, HigA family; Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair. [Regulatory functions, DNA interactions, Regulatory functions, Protein interactions, Mobile and extrachromosomal element functions, Other]


Pssm-ID: 274228 [Multi-domain]  Cd Length: 78  Bit Score: 37.60  E-value: 3.23e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 15599272   13 GWSQAELAGKLEVSRQTVNAIETGRYDPSLPLAFKLARVFG 53
Cdd:TIGR02607 18 GLSVRALAKALGVSRSTLSRIVNGRAAITADMALRLAKALG 58
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-64 4.68e-27

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 92.60  E-value: 4.68e-27
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15599272  1 MRNRVRELRAERGWSQAELAGKLEVSRQTVNAIETGRYDPSLPLAFKLARVFGLAIEAIFDDRE 64
Cdd:COG1476  5 LGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
3-68 1.42e-16

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 66.56  E-value: 1.42e-16
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15599272  3 NRVRELRAERGWSQAELAGKLEVSRQTVNAIETGRYDPSLPLAFKLARVFGLAIEAIFDDREGQLD 68
Cdd:COG1396 10 ERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELP 75
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
4-59 1.98e-16

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 65.62  E-value: 1.98e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 15599272     4 RVRELRAERGWSQAELAGKLEVSRQTVNAIETGRYDPSLPLAFKLARVFGLAIEAI 59
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 3-59 8.07e-16

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: 64.11  E-value: 8.07e-16
                       10        20        30        40        50
               ....*....|....*....|....*....|....*....|....*....|....*..
gi 15599272  3 NRVRELRAERGWSQAELAGKLEVSRQTVNAIETGRYDPSLPLAFKLARVFGLAIEAI 59
Cdd:cd00093  2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 4-57 8.87e-15

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: 61.88  E-value: 8.87e-15
                       10        20        30        40        50
               ....*....|....*....|....*....|....*....|....*....|....
gi 15599272  4 RVRELRAERGWSQAELAGKLEVSRQTVNAIETGRYDPSLPLAFKLARVFGLAIE 57
Cdd:COG1813 16 RIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLA 69
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 5-59 6.79e-14

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: 59.09  E-value: 6.79e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 15599272    5 VRELRAERGWSQAELAGKLEVSRQTVNAIETGRYDPSLPLAFKLARVFGLAIEAI 59
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 4-60 3.64e-11

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: 52.29  E-value: 3.64e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 15599272    4 RVRELRAERGWSQAELAGKLEVSRQTVNAIETGRYDPSLPLAFKLARVFGLAIEAIF 60
Cdd:pfam12844  3 RLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLL 59
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 6-57 2.46e-10

Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense mechanisms];


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 50.96  E-value: 2.46e-10
                       10        20        30        40        50
               ....*....|....*....|....*....|....*....|....*....|..
gi 15599272  6 RELRAERGWSQAELAGKLEVSRQTVNAIETGRYDPSLPLAFKLARVFGLAIE 57
Cdd:COG3093 15 EEFLEPLGLSQTELAKALGVSRQRISEILNGKRAITADTALRLARAFGTSAE 66
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 5-67 3.09e-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: 48.48  E-value: 3.09e-09
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15599272  5 VRELRAERGWSQAELAGKLEVSRQTVNAIETGRYDPSLPLAFKLARVFGLAIEAIFDDREGQL 67
Cdd:COG3620 22 LRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVLVVDDGKL 84
COG1395 COG1395
Predicted transcriptional regulator [Transcription];
6-56 5.96e-08

Predicted transcriptional regulator [Transcription];


Pssm-ID: 441005 [Multi-domain]  Cd Length: 313  Bit Score: 47.14  E-value: 5.96e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 15599272   6 RELRAERGWSQAELAGKLEVSRQTVNAIETGRYDPSLPLAFKLARVFGLAI 56
Cdd:COG1395 133 RELREERGLSLGELASELGVSRRTISKYERGEMDASIEVALKLEEILGEPI 183
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
4-59 1.51e-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: 1.51e-07
                       10        20        30        40        50
               ....*....|....*....|....*....|....*....|....*....|....*.
gi 15599272  4 RVRELRAERGWSQAELAGKLEVSRQTVNAIETGRYDPSLPlAFKLARVFGLAIEAI 59
Cdd:COG2944 10 EIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGA-ALKLLRLLEKHPELL 64
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
1-61 4.35e-07

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 42.05  E-value: 4.35e-07
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15599272  1 MRNRVRELRAERGWSQAELAGKLEVSRQTVNAIETGR-YDPSLPLAFKLARVFGLAIEAIFD 61
Cdd:COG3655  2 IYVKLDELLAERGMTKKELAEATGISRATLSRLKNGKaKAVRLDTLEKICKALDCQPGDLLE 63
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 4-57 5.53e-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: 41.74  E-value: 5.53e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 15599272    4 RVRELRAERGWSQAELAGKLEVSRQTVNAIETGRYD-PSLPLAFKLARVFGLAIE 57
Cdd:pfam13560  5 RLRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGrPSPAVVERLARALGVDGA 59
PRK04140 PRK04140
transcriptional regulator;
3-56 7.35e-07

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 44.08  E-value: 7.35e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 15599272    3 NRVRELRAERGWSQAELAGKLEVSRQTVNAIETGRYDPSLPLAFKLARVFGLAI 56
Cdd:PRK04140 129 DVLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDVPL 182
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 4-60 8.26e-07

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: 41.33  E-value: 8.26e-07
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15599272  4 RVRELRAERGWSQAELAGKLEVSRQTVNAIETGRYDPSLPLAF------KLARVFGLAIEAIF 60
Cdd:COG1426  9 LLRQAREAKGLSLEDVAERTKISVSYLEAIEEGDFDALPGPVYvrgflrSYARALGLDPEELL 71
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 13-53 3.23e-05

addiction module antidote protein, HigA family; Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair. [Regulatory functions, DNA interactions, Regulatory functions, Protein interactions, Mobile and extrachromosomal element functions, Other]


Pssm-ID: 274228 [Multi-domain]  Cd Length: 78  Bit Score: 37.60  E-value: 3.23e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 15599272   13 GWSQAELAGKLEVSRQTVNAIETGRYDPSLPLAFKLARVFG 53
Cdd:TIGR02607 18 GLSVRALAKALGVSRSTLSRIVNGRAAITADMALRLAKALG 58
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 4-61 5.43e-05

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: 36.75  E-value: 5.43e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 15599272    4 RVRELRAERGWSQAELAGKLEVSRQTVNAIETGRYD-PSLPLAFKLARVFGLAIEAIFD 61
Cdd:pfam13443  1 KLRKLMADRGISKSDLARATGISRATLSRLRKGKPKrVSLDTLDKICDALGCQPGDLLE 59
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
4-64 3.71e-04

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 36.31  E-value: 3.71e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15599272    4 RVRELRAERGWSQ---AELAGkleVSRQTVNAIETGRYDPSLPLAFKLARVFGLAIEAIFDDRE 64
Cdd:PRK09943  11 RLSEIRQQQGLSQrraAELSG---LTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFFSEPE 71
HTH_25 pfam13413
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 6-43 1.27e-03

Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.


Pssm-ID: 433187 [Multi-domain]  Cd Length: 62  Bit Score: 33.24  E-value: 1.27e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 15599272    6 RELRAERGWSQAELAGKLEVSRQTVNAIETGRYDpSLP 43
Cdd:pfam13413  3 RAAREARGLSLEDVAERTKIRPRYLEALEEDDFD-ALP 39
tfx TIGR00721
DNA-binding protein, Tfx family; PSI-BLAST starting with one member of this family converges ...
 4-34 4.35e-03

DNA-binding protein, Tfx family; PSI-BLAST starting with one member of this family converges with significant hits only to other members of the family, which is restricted to the Archaea. Homology is strongest in the helix-turn-helix-containing N-terminal region. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter. [Regulatory functions, DNA interactions]


Pssm-ID: 129804 [Multi-domain]  Cd Length: 137  Bit Score: 32.93  E-value: 4.35e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15599272     4 RVRELRaERGWSQAELAGKLEVSRQTVNAIE 34
Cdd:TIGR00721  13 KVLELR-EKGLSQKEIAKELKTTRANVSAIE 42
DeoR COG2390
DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];
4-54 8.10e-03

DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];


Pssm-ID: 441955 [Multi-domain]  Cd Length: 301  Bit Score: 32.41  E-value: 8.10e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15599272   4 RVRELRAERGWSQAELAGKLEVSRQTVN-----AIETG--------RYDPSLPLAFKLARVFGL 54
Cdd:COG2390   1 RAAWLYYVEGLTQREIAERLGISRRTVSrllaeAREEGlvrisitdPLAGLLELERELRERFGL 64
 
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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