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Conserved domains on  [gi|502864504|ref|WP_013099480|]
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helix-turn-helix domain-containing protein [Methanocaldococcus infernus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
COG1709 COG1709
Predicted transcriptional regulator,contains XRE-type HTH domain [Transcription];
1-229 2.04e-131

Predicted transcriptional regulator,contains XRE-type HTH domain [Transcription];


:

Pssm-ID: 441315  Cd Length: 234  Bit Score: 369.51  E-value: 2.04e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502864504   1 MEKVAIYIIGDIVLSECPGSVLKKWRKLFNIQQTELAKYLNVSPSVISDYETGRRKNPGASFIRKYVLALIEIDKNKGGK 80
Cdd:COG1709    6 REELAEKIAGEITLSDDPGETLRKWREDFGISQTELARELGVSPSVISDYESGRRKSPGIAFVKKFVEALLEIDEERGGK 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502864504  81 TVKALKRMLEKSPSMRAILDMKEYPKPISLEEFVETIDGTLLTEGDA--QIYGHTVIDSLKAIKELSGEEFYHLYGWTTE 158
Cdd:COG1709   86 VIRQLARVLSAGFDSDAILDIREYSSPVPLEEFVDAIDGTLVVSGDLdrRIYGYTVIDSIKAILELSSEEFYRLYGWSTE 165

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 502864504 159 RALIFTNVSSGRSPLVAIRVSPMKPRVIVLQGIlkNRVDKLAIELAKIDKIPLVVTNLDIEELIKRLSEIE 229
Cdd:COG1709  166 RALIFTNVSTGRSPMVAIRVSPLKPAAVVLHGP--DKVDPLAIKLAEIEGIPLIVTTLDIEELLKRLRELK 234
 
Name Accession Description Interval E-value
COG1709 COG1709
Predicted transcriptional regulator,contains XRE-type HTH domain [Transcription];
1-229 2.04e-131

Predicted transcriptional regulator,contains XRE-type HTH domain [Transcription];


Pssm-ID: 441315  Cd Length: 234  Bit Score: 369.51  E-value: 2.04e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502864504   1 MEKVAIYIIGDIVLSECPGSVLKKWRKLFNIQQTELAKYLNVSPSVISDYETGRRKNPGASFIRKYVLALIEIDKNKGGK 80
Cdd:COG1709    6 REELAEKIAGEITLSDDPGETLRKWREDFGISQTELARELGVSPSVISDYESGRRKSPGIAFVKKFVEALLEIDEERGGK 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502864504  81 TVKALKRMLEKSPSMRAILDMKEYPKPISLEEFVETIDGTLLTEGDA--QIYGHTVIDSLKAIKELSGEEFYHLYGWTTE 158
Cdd:COG1709   86 VIRQLARVLSAGFDSDAILDIREYSSPVPLEEFVDAIDGTLVVSGDLdrRIYGYTVIDSIKAILELSSEEFYRLYGWSTE 165

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 502864504 159 RALIFTNVSSGRSPLVAIRVSPMKPRVIVLQGIlkNRVDKLAIELAKIDKIPLVVTNLDIEELIKRLSEIE 229
Cdd:COG1709  166 RALIFTNVSTGRSPMVAIRVSPLKPAAVVLHGP--DKVDPLAIKLAEIEGIPLIVTTLDIEELLKRLRELK 234
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 19-70 1.26e-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: 49.86  E-value: 1.26e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 502864504  19 GSVLKKWRKLFNIQQTELAKYLNVSPSVISDYETGRRkNPGASFIRKYVLAL 70
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKR-NPSLETLEKLAKAL 51
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
22-70 1.94e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 49.44  E-value: 1.94e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 502864504    22 LKKWRKLFNIQQTELAKYLNVSPSVISDYETGRRKnPGASFIRKYVLAL 70
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRK-PSLETLKKLAKAL 49
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 22-70 3.28e-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: 3.28e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 502864504   22 LKKWRKLFNIQQTELAKYLNVSPSVISDYETGRRkNPGASFIRKYVLAL 70
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKR-EPSLETLKKLAEAL 48
 
Name Accession Description Interval E-value
COG1709 COG1709
Predicted transcriptional regulator,contains XRE-type HTH domain [Transcription];
1-229 2.04e-131

Predicted transcriptional regulator,contains XRE-type HTH domain [Transcription];


Pssm-ID: 441315  Cd Length: 234  Bit Score: 369.51  E-value: 2.04e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502864504   1 MEKVAIYIIGDIVLSECPGSVLKKWRKLFNIQQTELAKYLNVSPSVISDYETGRRKNPGASFIRKYVLALIEIDKNKGGK 80
Cdd:COG1709    6 REELAEKIAGEITLSDDPGETLRKWREDFGISQTELARELGVSPSVISDYESGRRKSPGIAFVKKFVEALLEIDEERGGK 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502864504  81 TVKALKRMLEKSPSMRAILDMKEYPKPISLEEFVETIDGTLLTEGDA--QIYGHTVIDSLKAIKELSGEEFYHLYGWTTE 158
Cdd:COG1709   86 VIRQLARVLSAGFDSDAILDIREYSSPVPLEEFVDAIDGTLVVSGDLdrRIYGYTVIDSIKAILELSSEEFYRLYGWSTE 165

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 502864504 159 RALIFTNVSSGRSPLVAIRVSPMKPRVIVLQGIlkNRVDKLAIELAKIDKIPLVVTNLDIEELIKRLSEIE 229
Cdd:COG1709  166 RALIFTNVSTGRSPMVAIRVSPLKPAAVVLHGP--DKVDPLAIKLAEIEGIPLIVTTLDIEELLKRLRELK 234
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 19-70 1.26e-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: 49.86  E-value: 1.26e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 502864504  19 GSVLKKWRKLFNIQQTELAKYLNVSPSVISDYETGRRkNPGASFIRKYVLAL 70
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKR-NPSLETLEKLAKAL 51
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
22-70 1.94e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 49.44  E-value: 1.94e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 502864504    22 LKKWRKLFNIQQTELAKYLNVSPSVISDYETGRRKnPGASFIRKYVLAL 70
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRK-PSLETLKKLAKAL 49
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
19-70 4.60e-08

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 48.84  E-value: 4.60e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 502864504  19 GSVLKKWRKLFNIQQTELAKYLNVSPSVISDYETGRRkNPGASFIRKYVLAL 70
Cdd:COG1396    9 GERLRELRKARGLTQEELAERLGVSRSTISRIERGRR-NPSLETLLKLAKAL 59
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 22-70 3.28e-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: 3.28e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 502864504   22 LKKWRKLFNIQQTELAKYLNVSPSVISDYETGRRkNPGASFIRKYVLAL 70
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKR-EPSLETLKKLAEAL 48
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
22-73 2.87e-06

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 43.38  E-value: 2.87e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 502864504  22 LKKWRKLFNIQQTELAKYLNVSPSVISDYETGRRKNPGAsfirkyVLALIEI 73
Cdd:COG2944   11 IRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGA------ALKLLRL 56
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
19-70 6.53e-06

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 42.53  E-value: 6.53e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 502864504  19 GSVLKKWRKLFNIQQTELAKYLNVSPSVISDYETGRRkNPGASFIRKYVLAL 70
Cdd:COG1476    6 GNRLKELRKERGLTQEELAELLGVSRQTISAIENGKY-NPSLELALKIARAL 56
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 19-65 2.28e-05

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: 41.08  E-value: 2.28e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 502864504  19 GSVLKKWRKLFNIQQTELAKYLNVSPSVISDYETGRRkNPGASFIRK 65
Cdd:COG1813   14 GERIREAREARGLSQEELAEKLGVSESTIRRIERGEA-TPSLDTLRK 59
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 33-64 1.36e-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: 35.97  E-value: 1.36e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 502864504   33 QTELAKYLNVSPSVISDYETGRRKNPGASFIR 64
Cdd:pfam13560  17 QEALARRLGVSRSTLSRLETGRRGRPSPAVVE 48
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 19-70 1.40e-03

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: 36.92  E-value: 1.40e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 502864504  19 GSVLKKWRKLFNIQQTELAKYLNVSPSVISDYETGRRkNPGASFIRKYVLAL 70
Cdd:COG3620   19 GEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKR-DPTVSTLEKIAEAL 69
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 18-55 2.73e-03

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 35.94  E-value: 2.73e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 502864504  18 PGSVLKKWR-KLFNIQQTELAKYLNVSPSVISDYETGRR 55
Cdd:COG3093    9 PGEILREEFlEPLGLSQTELAKALGVSRQRISEILNGKR 47
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 19-70 7.44e-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: 34.19  E-value: 7.44e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 502864504   19 GSVLKKWRKLFNIQQTELAKYLNVSPSVISDYETGRRKnPGASFIRKYVLAL 70
Cdd:pfam12844   1 GERLRKAREERGLTQEELAERLGISRSQLSAIENGKSV-PPAETLYKIAELL 51
 
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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