NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|494113862|ref|WP_007054640|]
View 

MULTISPECIES: helix-turn-helix transcriptional regulator [Bifidobacterium]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
155-216 3.09e-10

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


:

Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 54.47  E-value: 3.09e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 494113862 155 RLHTIRVRAGLSQSGLARRSGVTLRSIQMYEQRRKDLGkaaVSTVLALARTLGCRIEDLLEP 216
Cdd:COG1476    8 RLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPS---LELALKIARALGVSLEELFSL 66
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
155-216 3.09e-10

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 54.47  E-value: 3.09e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 494113862 155 RLHTIRVRAGLSQSGLARRSGVTLRSIQMYEQRRKDLGkaaVSTVLALARTLGCRIEDLLEP 216
Cdd:COG1476    8 RLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPS---LELALKIARALGVSLEELFSL 66
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
155-213 1.19e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 49.82  E-value: 1.19e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 494113862   155 RLHTIRVRAGLSQSGLARRSGVTLRSIQMYEQRRKdlgKAAVSTVLALARTLGCRIEDL 213
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKR---KPSLETLKKLAKALGVSLDEL 56
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 154-213 5.88e-08

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: 47.93  E-value: 5.88e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 494113862 154 SRLHTIRVRAGLSQSGLARRSGVTLRSIQMYEQrrkdlGKAAVS--TVLALARTLGCRIEDL 213
Cdd:cd00093    2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIEN-----GKRNPSleTLEKLAKALGVSLDEL 58
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 156-213 2.68e-07

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: 45.99  E-value: 2.68e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 494113862  156 LHTIRVRAGLSQSGLARRSGVTLRSIQMYEqrrKDLGKAAVSTVLALARTLGCRIEDL 213
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIE---NGKREPSLETLKKLAEALGVSLDEL 55
PRK08154 PRK08154
anaerobic benzoate catabolism transcriptional regulator; Reviewed
 155-216 2.92e-03

anaerobic benzoate catabolism transcriptional regulator; Reviewed


Pssm-ID: 236167 [Multi-domain]  Cd Length: 309  Bit Score: 38.01  E-value: 2.92e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 494113862 155 RLHTIRVRAGLSQSGLARRSGVTLRSIQMYEQrrkdlGKAAVSTVL--ALARTLGCRIEDLLEP 216
Cdd:PRK08154  32 RVRTLRARRGMSRKVLAQASGVSERYLAQLES-----GQGNVSILLlrRVARALGCSLADLLGD 90
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
155-216 3.09e-10

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 54.47  E-value: 3.09e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 494113862 155 RLHTIRVRAGLSQSGLARRSGVTLRSIQMYEQRRKDLGkaaVSTVLALARTLGCRIEDLLEP 216
Cdd:COG1476    8 RLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPS---LELALKIARALGVSLEELFSL 66
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
155-216 8.74e-09

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 50.77  E-value: 8.74e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 494113862 155 RLHTIRVRAGLSQSGLARRSGVTLRSIQMYEQRRKdlgKAAVSTVLALARTLGCRIEDLLEP 216
Cdd:COG1396   11 RLRELRKARGLTQEELAERLGVSRSTISRIERGRR---NPSLETLLKLAKALGVSLDELLGG 69
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
155-213 1.19e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 49.82  E-value: 1.19e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 494113862   155 RLHTIRVRAGLSQSGLARRSGVTLRSIQMYEQRRKdlgKAAVSTVLALARTLGCRIEDL 213
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKR---KPSLETLKKLAKALGVSLDEL 56
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 154-213 5.88e-08

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: 47.93  E-value: 5.88e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 494113862 154 SRLHTIRVRAGLSQSGLARRSGVTLRSIQMYEQrrkdlGKAAVS--TVLALARTLGCRIEDL 213
Cdd:cd00093    2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIEN-----GKRNPSleTLEKLAKALGVSLDEL 58
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 156-213 2.68e-07

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: 45.99  E-value: 2.68e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 494113862  156 LHTIRVRAGLSQSGLARRSGVTLRSIQMYEqrrKDLGKAAVSTVLALARTLGCRIEDL 213
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIE---NGKREPSLETLKKLAEALGVSLDEL 55
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 156-214 1.02e-06

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: 45.40  E-value: 1.02e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 494113862 156 LHTIRVRAGLSQSGLARRSGVTLRSIQMYEQRRKDlgkAAVSTVLALARTLGCRIEDLL 214
Cdd:COG3620   22 LRLMRKELGLSQLPVAELVGVSQSDILRIESGKRD---PTVSTLEKIAEALGKELSAVL 77
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
155-215 4.72e-05

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 40.13  E-value: 4.72e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 494113862 155 RLHTIRVRAGLSQSGLARRSGVTLRSIQ-MYEQRRKDLGkaaVSTVLALARTLGCRIEDLLE 215
Cdd:COG3655    5 KLDELLAERGMTKKELAEATGISRATLSrLKNGKAKAVR---LDTLEKICKALDCQPGDLLE 63
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 155-216 1.49e-04

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: 38.68  E-value: 1.49e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 494113862  155 RLHTIRVRAGLSQSGLARRSGVTLRSIQMYEQRRKDlgKAAVSTVLALARTLGCRIEDLLEP 216
Cdd:pfam13443   1 KLRKLMADRGISKSDLARATGISRATLSRLRKGKPK--RVSLDTLDKICDALGCQPGDLLEY 60
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 155-207 3.82e-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: 37.51  E-value: 3.82e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 494113862  155 RLHTIRVRAGLSQSGLARRSGVTLRSIQMYEQRRKDLGKAAVstVLALARTLG 207
Cdd:pfam13560   5 RLRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGRPSPAV--VERLARALG 55
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
155-196 6.55e-04

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 36.84  E-value: 6.55e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 494113862 155 RLHTIRVRAGLSQSGLARRSGVTLRSIQMYEQRRKDLGKAAV 196
Cdd:COG2944   10 EIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAAL 51
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 154-212 7.99e-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: 36.84  E-value: 7.99e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 494113862 154 SRLHTIRVRAGLSQSGLARRSGVTLRSIQMYEQrrkdlGKAAVS--TVLALARTLGCRIED 212
Cdd:COG1813   15 ERIREAREARGLSQEELAEKLGVSESTIRRIER-----GEATPSldTLRKLEKALGISLAE 70
COG1395 COG1395
Predicted transcriptional regulator [Transcription];
155-216 1.32e-03

Predicted transcriptional regulator [Transcription];


Pssm-ID: 441005 [Multi-domain]  Cd Length: 313  Bit Score: 39.05  E-value: 1.32e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 494113862 155 RLHTIRVRAGLSQSGLARRSGVTLRSIQMYEQRRKDlgkAAVSTVLALARTLGcriEDLLEP 216
Cdd:COG1395  131 KLRELREERGLSLGELASELGVSRRTISKYERGEMD---ASIEVALKLEEILG---EPIVKP 186
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 155-214 2.68e-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: 35.34  E-value: 2.68e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 494113862  155 RLHTIRVRAGLSQSGLARRSGVTLRSIQMYEQRRKDLGKaavSTVLALARTLGCRIEDLL 214
Cdd:pfam12844   3 RLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPA---ETLYKIAELLGVPANWLL 59
PRK08154 PRK08154
anaerobic benzoate catabolism transcriptional regulator; Reviewed
 155-216 2.92e-03

anaerobic benzoate catabolism transcriptional regulator; Reviewed


Pssm-ID: 236167 [Multi-domain]  Cd Length: 309  Bit Score: 38.01  E-value: 2.92e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 494113862 155 RLHTIRVRAGLSQSGLARRSGVTLRSIQMYEQrrkdlGKAAVSTVL--ALARTLGCRIEDLLEP 216
Cdd:PRK08154  32 RVRTLRARRGMSRKVLAQASGVSERYLAQLES-----GQGNVSILLlrRVARALGCSLADLLGD 90
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
155-207 6.42e-03

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 36.31  E-value: 6.42e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 494113862 155 RLHTIRVRAGLSQSGLARRSGVTLRSIQMYEQrrkDLGKAAVSTVLALARTLG 207
Cdd:PRK09943  11 RLSEIRQQQGLSQRRAAELSGLTHSAISTIEQ---DKVSPAISTLQKLLKVYG 60
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH