NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|896491076|ref|WP_049400816|]
View 

MULTISPECIES: helix-turn-helix domain-containing protein [Stenotrophomonas]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 11443570)

helix-turn-helix domain-containing protein such as an XRE (Xenobiotic Response Element) family transcriptional regulator

Gene Ontology:  GO:0003677
PubMed:  37972151

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-70 3.44e-14

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 62.32  E-value: 3.44e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896491076   1 MEFRTDSLSARIRVARISNGLSQTDLAKALNVNRATVGHWERELGfVPSIDHLHALSRVTCVSVSWLITG 70
Cdd:COG1396    1 MSTLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRR-NPSLETLLKLAKALGVSLDELLGG 69
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-70 3.44e-14

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 62.32  E-value: 3.44e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896491076   1 MEFRTDSLSARIRVARISNGLSQTDLAKALNVNRATVGHWERELGfVPSIDHLHALSRVTCVSVSWLITG 70
Cdd:COG1396    1 MSTLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRR-NPSLETLLKLAKALGVSLDELLGG 69
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 11-67 2.72e-10

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: 51.78  E-value: 2.72e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 896491076  11 RIRVARISNGLSQTDLAKALNVNRATVGHWERElGFVPSIDHLHALSRVTCVSVSWL 67
Cdd:cd00093    3 RLKELRKEKGLTQEELAEKLGVSRSTISRIENG-KRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
11-67 9.09e-09

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 47.90  E-value: 9.09e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 896491076    11 RIRVARISNGLSQTDLAKALNVNRATVGHWERElGFVPSIDHLHALSRVTCVSVSWL 67
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENG-KRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 12-67 1.13e-08

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: 47.54  E-value: 1.13e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 896491076   12 IRVARISNGLSQTDLAKALNVNRATVGHWERELGfVPSIDHLHALSRVTCVSVSWL 67
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKR-EPSLETLKKLAEALGVSLDEL 55
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 4-71 7.48e-08

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 47.54  E-value: 7.48e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 896491076   4 RTDSLSARIRVARISNGLSQTDLAKALNVNRATVGHWERELGfVPSIDHLHALSRVTCVSVSWLITGN 71
Cdd:PRK09706   2 KNLTLGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDET-EPTGKNLFALAKALQCSPTWLLFGD 68
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-70 3.44e-14

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 62.32  E-value: 3.44e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896491076   1 MEFRTDSLSARIRVARISNGLSQTDLAKALNVNRATVGHWERELGfVPSIDHLHALSRVTCVSVSWLITG 70
Cdd:COG1396    1 MSTLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRR-NPSLETLLKLAKALGVSLDELLGG 69
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
7-71 3.55e-13

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 59.48  E-value: 3.55e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 896491076   7 SLSARIRVARISNGLSQTDLAKALNVNRATVGHWERElGFVPSIDHLHALSRVTCVSVSWLITGN 71
Cdd:COG1476    4 KLGNRLKELRKERGLTQEELAELLGVSRQTISAIENG-KYNPSLELALKIARALGVSLEELFSLE 67
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 11-67 2.72e-10

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: 51.78  E-value: 2.72e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 896491076  11 RIRVARISNGLSQTDLAKALNVNRATVGHWERElGFVPSIDHLHALSRVTCVSVSWL 67
Cdd:cd00093    3 RLKELRKEKGLTQEELAEKLGVSRSTISRIENG-KRNPSLETLEKLAKALGVSLDEL 58
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 5-59 2.68e-09

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: 49.55  E-value: 2.68e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 896491076   5 TDSLSARIRVARISNGLSQTDLAKALNVNRATVGHWERELgFVPSIDHLHALSRV 59
Cdd:COG1813   10 VEDYGERIREAREARGLSQEELAEKLGVSESTIRRIERGE-ATPSLDTLRKLEKA 63
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
11-67 9.09e-09

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 47.90  E-value: 9.09e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 896491076    11 RIRVARISNGLSQTDLAKALNVNRATVGHWERElGFVPSIDHLHALSRVTCVSVSWL 67
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENG-KRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 12-67 1.13e-08

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: 47.54  E-value: 1.13e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 896491076   12 IRVARISNGLSQTDLAKALNVNRATVGHWERELGfVPSIDHLHALSRVTCVSVSWL 67
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKR-EPSLETLKKLAEALGVSLDEL 55
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 4-71 7.48e-08

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 47.54  E-value: 7.48e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 896491076   4 RTDSLSARIRVARISNGLSQTDLAKALNVNRATVGHWERELGfVPSIDHLHALSRVTCVSVSWLITGN 71
Cdd:PRK09706   2 KNLTLGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDET-EPTGKNLFALAKALQCSPTWLLFGD 68
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 8-63 6.53e-06

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: 40.59  E-value: 6.53e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 896491076    8 LSARIRVARISNGLSQTDLAKALNVNRATVGHWERELGFVPSIDHLHALSRVTCVS 63
Cdd:pfam13560   2 LGARLRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGRPSPAVVERLARALGVD 57
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
1-42 9.05e-06

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 40.30  E-value: 9.05e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 896491076   1 MEFRTDSlSARIRVARISNGLSQTDLAKALNVNRATVGHWER 42
Cdd:COG2944    1 MTKKPLT-PEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQ 41
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 5-81 2.56e-04

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: 37.31  E-value: 2.56e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 896491076   5 TDSLSARIRVARISNGLSQTDLAKALNVNRATVGHWERELGfVPSIDHLHALSRVTCVSVSWLItgntIADGGKPEG 81
Cdd:COG3620   15 DDTLGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKR-DPTVSTLEKIAEALGKELSAVL----VVDDGKLVG 86
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 11-70 3.42e-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: 36.11  E-value: 3.42e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 896491076   11 RIRVARISNGLSQTDLAKALNVNRATVGHWERELgFVPSIDHLHALSRVTCVSVSWLITG 70
Cdd:pfam12844   3 RLRKAREERGLTQEELAERLGISRSQLSAIENGK-SVPPAETLYKIAELLGVPANWLLQG 61
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 11-59 1.25e-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: 34.82  E-value: 1.25e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 896491076   11 RIRVARISNGLSQTDLAKALNVNRATVGHWERELGFVPSIDHLHALSRV 59
Cdd:pfam13443   1 KLRKLMADRGISKSDLARATGISRATLSRLRKGKPKRVSLDTLDKICDA 49
PRK13355 PRK13355
bifunctional HTH-domain containing protein/aminotransferase; Provisional
 7-76 3.42e-03

bifunctional HTH-domain containing protein/aminotransferase; Provisional


Pssm-ID: 237361 [Multi-domain]  Cd Length: 517  Bit Score: 35.48  E-value: 3.42e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 896491076   7 SLSARIRVARISNGLSQTDLAKALN-----VNRATVGHWERELGfVPSIDHLHALSRVTCVSVSWLITGNTIADG 76
Cdd:PRK13355   3 TFAERLKQAMKARGLKQEDLVHAAEargvkLGKSHISQYVSGKT-GPRRDVLPFLAAILGVSEDWLLGGESPADQ 76
 
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