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Conserved domains on  [gi|218431204|emb|CAR12081|]
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putative phage replication protein O [Escherichia coli UMN026]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 10617438)

helix-turn-helix (HTH) domain-containing protein binds DNA and may function as a transcriptional regulator

Gene Ontology:  GO:0003677
PubMed:  15808743

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_36 pfam13730
Helix-turn-helix domain;
17-70 1.84e-10

Helix-turn-helix domain;


:

Pssm-ID: 463970 [Multi-domain]  Cd Length: 55  Bit Score: 55.57  E-value: 1.84e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 218431204   17 GMKLSSVAIMARLADFSNDEGVCWPSIETIARQIGAGMSTVRTAIARLEAEGWL 70
Cdd:pfam13730   2 RLSPTAKLLLLILASYANKDGGCFPSVETLAKRLGLSRRTIQRAIKELEELGYL 55
 
Name Accession Description Interval E-value
HTH_36 pfam13730
Helix-turn-helix domain;
17-70 1.84e-10

Helix-turn-helix domain;


Pssm-ID: 463970 [Multi-domain]  Cd Length: 55  Bit Score: 55.57  E-value: 1.84e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 218431204   17 GMKLSSVAIMARLADFSNDEGVCWPSIETIARQIGAGMSTVRTAIARLEAEGWL 70
Cdd:pfam13730   2 RLSPTAKLLLLILASYANKDGGCFPSVETLAKRLGLSRRTIQRAIKELEELGYL 55
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 41-76 1.26e-06

Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is presumed to result in a conformational change that regulates the DNA-binding affinity of the repressor. The GntR-like proteins bind as dimers, where each monomer recognizes a half-site of 2-fold symmetric DNA sequences.


Pssm-ID: 153418 [Multi-domain]  Cd Length: 66  Bit Score: 45.13  E-value: 1.26e-06
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 218431204  41 PSIETIARQIGAGMSTVRTAIARLEAEGWLTRKARR 76
Cdd:cd07377   26 PSERELAEELGVSRTTVREALRELEAEGLVERRPGR 61
HTH_GNTR smart00345
helix_turn_helix gluconate operon transcriptional repressor;
41-76 3.53e-05

helix_turn_helix gluconate operon transcriptional repressor;


Pssm-ID: 197669 [Multi-domain]  Cd Length: 60  Bit Score: 41.02  E-value: 3.53e-05
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 218431204    41 PSIETIARQIGAGMSTVRTAIARLEAEGWLTRKARR 76
Cdd:smart00345  21 PSERELAAQLGVSRTTVREALSRLEAEGLVQRRPGS 56
GntR COG1802
DNA-binding transcriptional regulator, GntR family [Transcription];
42-76 6.70e-05

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


Pssm-ID: 441407 [Multi-domain]  Cd Length: 222  Bit Score: 43.37  E-value: 6.70e-05
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 218431204  42 SIETIARQIGAGMSTVRTAIARLEAEGWLTRKARR 76
Cdd:COG1802   36 SEAELAERLGVSRTPVREALRRLEAEGLVEIRPNR 70
 
Name Accession Description Interval E-value
HTH_36 pfam13730
Helix-turn-helix domain;
17-70 1.84e-10

Helix-turn-helix domain;


Pssm-ID: 463970 [Multi-domain]  Cd Length: 55  Bit Score: 55.57  E-value: 1.84e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 218431204   17 GMKLSSVAIMARLADFSNDEGVCWPSIETIARQIGAGMSTVRTAIARLEAEGWL 70
Cdd:pfam13730   2 RLSPTAKLLLLILASYANKDGGCFPSVETLAKRLGLSRRTIQRAIKELEELGYL 55
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 41-76 1.26e-06

Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is presumed to result in a conformational change that regulates the DNA-binding affinity of the repressor. The GntR-like proteins bind as dimers, where each monomer recognizes a half-site of 2-fold symmetric DNA sequences.


Pssm-ID: 153418 [Multi-domain]  Cd Length: 66  Bit Score: 45.13  E-value: 1.26e-06
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 218431204  41 PSIETIARQIGAGMSTVRTAIARLEAEGWLTRKARR 76
Cdd:cd07377   26 PSERELAEELGVSRTTVREALRELEAEGLVERRPGR 61
GntR pfam00392
Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the ...
 41-76 1.13e-05

Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerization domain. The GntR-like proteins include the following sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA, DevA, DasR. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships. The DasR regulator has been shown to be a global regulator of primary metabolism and development in Streptomyces coelicolor.


Pssm-ID: 306822 [Multi-domain]  Cd Length: 64  Bit Score: 42.22  E-value: 1.13e-05
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 218431204   41 PSIETIARQIGAGMSTVRTAIARLEAEGWLTRKARR 76
Cdd:pfam00392  25 PSERELAAEFGVSRTTVREALRRLEAEGLVERRQGR 60
HTH_GNTR smart00345
helix_turn_helix gluconate operon transcriptional repressor;
41-76 3.53e-05

helix_turn_helix gluconate operon transcriptional repressor;


Pssm-ID: 197669 [Multi-domain]  Cd Length: 60  Bit Score: 41.02  E-value: 3.53e-05
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 218431204    41 PSIETIARQIGAGMSTVRTAIARLEAEGWLTRKARR 76
Cdd:smart00345  21 PSERELAAQLGVSRTTVREALSRLEAEGLVQRRPGS 56
GntR COG1802
DNA-binding transcriptional regulator, GntR family [Transcription];
42-76 6.70e-05

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


Pssm-ID: 441407 [Multi-domain]  Cd Length: 222  Bit Score: 43.37  E-value: 6.70e-05
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 218431204  42 SIETIARQIGAGMSTVRTAIARLEAEGWLTRKARR 76
Cdd:COG1802   36 SEAELAERLGVSRTPVREALRRLEAEGLVEIRPNR 70
RP-C pfam03428
Replication protein C N-terminal domain; Replication protein C is involved in the early stages ...
 30-80 2.20e-03

Replication protein C N-terminal domain; Replication protein C is involved in the early stages of viral DNA replication.


Pssm-ID: 427291 [Multi-domain]  Cd Length: 174  Bit Score: 38.37  E-value: 2.20e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 218431204   30 ADFSNDEG-VCWPSIETIARQIGAGMSTVRTAIARLEAEGWLTRKARRQGNR 80
Cdd:pfam03428  59 DDWSEGARpIVFPSNAQLSRAHGMSESTLRRHLRRLVEAGLIARRDSPNGKR 110
PaaX pfam07848
PaaX-like protein; This family contains proteins that are similar to the product of the paaX ...
 50-80 5.40e-03

PaaX-like protein; This family contains proteins that are similar to the product of the paaX gene of Escherichia coli. This protein is involved in the regulation of expression of a group of proteins known to participate in the metabolism of phenylacetic acid. In fact, some members of this family are annotated by InterPro as containing a winged helix DNA-binding domain (Interpro:IPR009058).


Pssm-ID: 285132 [Multi-domain]  Cd Length: 70  Bit Score: 35.02  E-value: 5.40e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 218431204   50 IGAGMSTVRTAIARLEAEGWLTRKarRQGNR 80
Cdd:pfam07848  33 FGISERTVRTALSRLVKAGWLVRE--RTGRR 61
FadR COG2186
DNA-binding transcriptional regulator, FadR family [Transcription];
41-78 8.80e-03

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


Pssm-ID: 441789 [Multi-domain]  Cd Length: 232  Bit Score: 36.84  E-value: 8.80e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 218431204  41 PSIETIARQIGAGMSTVRTAIARLEAEGWLTrkaRRQG 78
Cdd:COG2186   32 PSERELAEQLGVSRTTVREALRALEALGLVE---VRQG 66
ARO8 COG1167
DNA-binding transcriptional regulator, MocR family, contains an aminotransferase domain ...
 41-76 8.98e-03

DNA-binding transcriptional regulator, MocR family, contains an aminotransferase domain [Transcription, Amino acid transport and metabolism]; DNA-binding transcriptional regulator, MocR family, contains an aminotransferase domain is part of the Pathway/BioSystem: Lysine biosynthesis


Pssm-ID: 440781 [Multi-domain]  Cd Length: 471  Bit Score: 37.50  E-value: 8.98e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 218431204  41 PSIETIARQIGAGMSTVRTAIARLEAEGWLTRKARR 76
Cdd:COG1167   37 PSSRELAAQLGVSRSTVVRAYEELEAEGLIESRPGS 72
 
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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