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Conserved domains on  [gi|499336236|ref|WP_011026259|]
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MULTISPECIES: helix-turn-helix transcriptional regulator [Caldanaerobacter]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 10650117)

helix-turn-helix (HTH) domain-containing protein with an XRE (Xenobiotic Response Element) family HTH domain, binds DNA and may function as a transcriptional regulator

CATH:  1.10.10.10
Gene Ontology:  GO:0003677
PubMed:  15808743|2644244|8831795
SCOP:  4000362

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
VapI super family cl42559
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 1-47 4.91e-05

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


The actual alignment was detected with superfamily member COG3093:

Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 37.10  E-value: 4.91e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 499336236  1 MKKRKLTEFGK-LVNDRLAELNMTQKELSQLIGTSEPYLSMILRGARS 47
Cdd:COG3093   1 MNKRNPIHPGEiLREEFLEPLGLSQTELAKALGVSRQRISEILNGKRA 48
 
Name Accession Description Interval E-value
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 1-47 4.91e-05

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 37.10  E-value: 4.91e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 499336236  1 MKKRKLTEFGK-LVNDRLAELNMTQKELSQLIGTSEPYLSMILRGARS 47
Cdd:COG3093   1 MNKRNPIHPGEiLREEFLEPLGLSQTELAKALGVSRQRISEILNGKRA 48
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
16-47 5.68e-04

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 33.65  E-value: 5.68e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 499336236   16 RLAELNMTQKELSQLIGTSEPYLSMILRGARS 47
Cdd:smart00530  5 LREEKGLTQEELAEKLGVSRSTLSRIENGKRK 36
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 10-47 3.48e-03

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: 31.75  E-value: 3.48e-03
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 499336236 10 GKLVNDRLAELNMTQKELSQLIGTSEPYLSMILRGARS 47
Cdd:cd00093   1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRN 38
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 19-47 6.29e-03

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: 30.97  E-value: 6.29e-03
                         10        20
                 ....*....|....*....|....*....
gi 499336236  19 ELNMTQKELSQLIGTSEPYLSMILRGARS 47
Cdd:pfam01381  7 ELGLSQEELAEKLGVSRSTISKIENGKRE 35
 
Name Accession Description Interval E-value
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 1-47 4.91e-05

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 37.10  E-value: 4.91e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 499336236  1 MKKRKLTEFGK-LVNDRLAELNMTQKELSQLIGTSEPYLSMILRGARS 47
Cdd:COG3093   1 MNKRNPIHPGEiLREEFLEPLGLSQTELAKALGVSRQRISEILNGKRA 48
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 7-47 1.81e-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: 35.77  E-value: 1.81e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 499336236  7 TEFGKLVNDRLAELNMTQKELSQLIGTSEPYLSMILRGARS 47
Cdd:COG3620  16 DTLGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRD 56
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
3-47 5.40e-04

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 34.20  E-value: 5.40e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 499336236  3 KRKLTEFGKLVNDRLAELNMTQKELSQLIGTSEPYLSMILRGARS 47
Cdd:COG1396   2 STLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRN 46
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
16-47 5.68e-04

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 33.65  E-value: 5.68e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 499336236   16 RLAELNMTQKELSQLIGTSEPYLSMILRGARS 47
Cdd:smart00530  5 LREEKGLTQEELAEKLGVSRSTLSRIENGKRK 36
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 10-47 3.48e-03

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: 31.75  E-value: 3.48e-03
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 499336236 10 GKLVNDRLAELNMTQKELSQLIGTSEPYLSMILRGARS 47
Cdd:cd00093   1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRN 38
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
8-47 5.10e-03

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 31.36  E-value: 5.10e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 499336236  8 EFGKLVNDRLAELNMTQKELSQLIGTSEPYLSMILRGARS 47
Cdd:COG1476   4 KLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYN 43
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 19-47 6.29e-03

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: 30.97  E-value: 6.29e-03
                         10        20
                 ....*....|....*....|....*....
gi 499336236  19 ELNMTQKELSQLIGTSEPYLSMILRGARS 47
Cdd:pfam01381  7 ELGLSQEELAEKLGVSRSTISKIENGKRE 35
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 7-44 6.65e-03

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: 31.06  E-value: 6.65e-03
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 499336236  7 TEFGKLVNDRLAELNMTQKELSQLIGTSEPYLSMILRG 44
Cdd:COG1813  11 EDYGERIREAREARGLSQEELAEKLGVSESTIRRIERG 48
HigA COG5499
Antitoxin component HigA of the HigAB toxin-antitoxin module, contains an N-terminal HTH ...
 16-47 9.38e-03

Antitoxin component HigA of the HigAB toxin-antitoxin module, contains an N-terminal HTH domain [Defense mechanisms];


Pssm-ID: 444250  Cd Length: 127  Bit Score: 31.72  E-value: 9.38e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 499336236  16 RLAELNMTQKELSQLIGtSEPYLSMILRGARS 47
Cdd:COG5499   73 LMEQHGLTQKDLAPEIG-SKSRVSEILNGKRS 103
 
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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