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Conserved domains on  [gi|906392220|gb|KNB78964|]
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XRE family transcriptional regulator [Bacillus subtilis]

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 7.02e-25

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


:

Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 87.21  E-value: 7.02e-25
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 906392220  1 MKNKVKELRARFGYSQEKLGETVGVTRQTVAAIEKGDYVPSLLLALKICKAFSMKMEDVFWLEE 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 7.02e-25

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 87.21  E-value: 7.02e-25
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 906392220  1 MKNKVKELRARFGYSQEKLGETVGVTRQTVAAIEKGDYVPSLLLALKICKAFSMKMEDVFWLEE 64
Cdd:COG1476   5 LGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
4-59 7.86e-13

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 56.37  E-value: 7.86e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 906392220    4 KVKELRARFGYSQEKLGETVGVTRQTVAAIEKGDYVPSLLLALKICKAFSMKMEDV 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 2.00e-12

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: 55.25  E-value: 2.00e-12
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 906392220  3 NKVKELRARFGYSQEKLGETVGVTRQTVAAIEKGDYVPSLLLALKICKAFSMKMEDV 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 ...
 5-52 7.88e-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: 51.39  E-value: 7.88e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 906392220   5 VKELRARFGYSQEKLGETVGVTRQTVAAIEKGDYVPSLLLALKICKAF 52
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEAL 48
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
1-66 1.17e-04

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 37.47  E-value: 1.17e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 906392220   1 MKNKVKELRARFGYSQEKLGETVGVTRQTVAAIEKGDYVPSLLLALKICKAFSMKMEDVFWLEEEN 66
Cdd:PRK09943   8 PGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFFSEPEKP 73
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 12-62 1.18e-04

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: 36.06  E-value: 1.18e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 906392220  12 FGYSQEKLGETVGVTRQTVAAIEKGDYVPSLLLALKICKAFSMKMEdvFWL 62
Cdd:TIGR02607 17 LGLSVRALAKALGVSRSTLSRIVNGRAAITADMALRLAKALGTSPE--FWL 65
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-64 7.02e-25

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 87.21  E-value: 7.02e-25
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 906392220  1 MKNKVKELRARFGYSQEKLGETVGVTRQTVAAIEKGDYVPSLLLALKICKAFSMKMEDVFWLEE 64
Cdd:COG1476   5 LGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
3-60 7.55e-13

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 56.93  E-value: 7.55e-13
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 906392220  3 NKVKELRARFGYSQEKLGETVGVTRQTVAAIEKGDYVPSLLLALKICKAFSMKMEDVF 60
Cdd:COG1396  10 ERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELL 67
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
4-59 7.86e-13

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 56.37  E-value: 7.86e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 906392220    4 KVKELRARFGYSQEKLGETVGVTRQTVAAIEKGDYVPSLLLALKICKAFSMKMEDV 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 2.00e-12

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: 55.25  E-value: 2.00e-12
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 906392220  3 NKVKELRARFGYSQEKLGETVGVTRQTVAAIEKGDYVPSLLLALKICKAFSMKMEDV 59
Cdd:cd00093   2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 4-58 1.11e-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: 53.79  E-value: 1.11e-11
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 906392220  4 KVKELRARFGYSQEKLGETVGVTRQTVAAIEKGDYVPSLLLALKICKAFSMKMED 58
Cdd:COG1813  16 RIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLAE 70
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 5-52 7.88e-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: 51.39  E-value: 7.88e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 906392220   5 VKELRARFGYSQEKLGETVGVTRQTVAAIEKGDYVPSLLLALKICKAF 52
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEAL 48
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 5-59 1.14e-08

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: 46.94  E-value: 1.14e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 906392220  5 VKELRARFGYSQEKLGETVGVTRQTVAAIEKGDYVPSLLLALKICKAFSMKMEDV 59
Cdd:COG3620  22 LRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAV 76
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 4-65 2.52e-07

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: 42.66  E-value: 2.52e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 906392220   4 KVKELRARFGYSQEKLGETVGVTRQTVAAIEKGDYVPSLLLALKICKAFSMKMEDVFWLEEE 65
Cdd:pfam12844  3 RLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLLQGEGE 64
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
5-41 1.16e-05

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 38.38  E-value: 1.16e-05
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 906392220  5 VKELRARFGYSQEKLGETVGVTRQTVAAIEKGDYVPS 41
Cdd:COG2944  11 IRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPS 47
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 7-62 1.05e-04

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 36.33  E-value: 1.05e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 906392220  7 ELRARFGYSQEKLGETVGVTRQTVAAIEKGDYVPSLLLALKICKAFSMKMEdvFWL 62
Cdd:COG3093  16 EFLEPLGLSQTELAKALGVSRQRISEILNGKRAITADTALRLARAFGTSAE--FWL 69
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
1-66 1.17e-04

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 37.47  E-value: 1.17e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 906392220   1 MKNKVKELRARFGYSQEKLGETVGVTRQTVAAIEKGDYVPSLLLALKICKAFSMKMEDVFWLEEEN 66
Cdd:PRK09943   8 PGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFFSEPEKP 73
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 12-62 1.18e-04

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: 36.06  E-value: 1.18e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 906392220  12 FGYSQEKLGETVGVTRQTVAAIEKGDYVPSLLLALKICKAFSMKMEdvFWL 62
Cdd:TIGR02607 17 LGLSVRALAKALGVSRSTLSRIVNGRAAITADMALRLAKALGTSPE--FWL 65
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 6-52 3.31e-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: 34.43  E-value: 3.31e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 906392220   6 KELRARFGYSQEKLGETVGVTRQTVAAIEKGDY-VPSLLLALKICKAF 52
Cdd:pfam13560  7 RRLRERAGLSQEALARRLGVSRSTLSRLETGRRgRPSPAVVERLARAL 54
PRK04140 PRK04140
transcriptional regulator;
3-48 2.22e-03

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 34.06  E-value: 2.22e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 906392220   3 NKVKELRARFGYSQEKLGETVGVTRQTVAAIEKGDYVPSLLLALKI 48
Cdd:PRK04140 129 DVLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKL 174
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 4-60 5.01e-03

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: 31.74  E-value: 5.01e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 906392220   4 KVKELRARFGYSQEKLGETVGVTRQTVAAIEKGD-YVPSLLLALKICKAFSMKMEDVF 60
Cdd:pfam13443  1 KLRKLMADRGISKSDLARATGISRATLSRLRKGKpKRVSLDTLDKICDALGCQPGDLL 58
COG1395 COG1395
Predicted transcriptional regulator [Transcription];
4-48 5.05e-03

Predicted transcriptional regulator [Transcription];


Pssm-ID: 441005 [Multi-domain]  Cd Length: 313  Bit Score: 32.89  E-value: 5.05e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 906392220   4 KVKELRARFGYSQEKLGETVGVTRQTVAAIEKGDYVPSLLLALKI 48
Cdd:COG1395  131 KLRELREERGLSLGELASELGVSRRTISKYERGEMDASIEVALKL 175
 
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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