Birnavirus RNA dependent RNA polymerase (VP1), palm domain; Birnaviruses are dsRNA viruses. This entry corresponds to the "palm" domain of the RNA dependent RNA polymerase, also known as VP1. All of the birnavirus VP1 proteins contain conserved RdRp motifs that reside in the catalytic "palm" domain of all classes of polymerases. However, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps. The catalytic motifs are arranged in a permuted order in sequence.
The actual alignment was detected with superfamily member pfam04197:
Pssm-ID: 461223 Cd Length: 531 Bit Score: 1000.26 E-value: 0e+00
Birnavirus RNA dependent RNA polymerase (VP1), thumb domain; Birnaviruses are dsRNA viruses. ...
523-687
1.40e-97
Birnavirus RNA dependent RNA polymerase (VP1), thumb domain; Birnaviruses are dsRNA viruses. The RNA dependent RNA polymerase, also known as VP1, contains the conserved RdRp motifs that reside in the catalytic "palm" domain of all classes of polymerases but in a characteriztic permuted order, thus, it adopts a unique active site topology. Additionally, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps. This entry covers the thumb domain of RdRP from Birnaviruses.
:
Pssm-ID: 466637 Cd Length: 167 Bit Score: 301.44 E-value: 1.40e-97
Birnavirus RNA dependent RNA polymerase (VP1), C-terminal; Birnaviruses are dsRNA viruses. This entry corresponds to the C-terminal domain of RNA dependent RNA polymerase also known as VP1. All of the birnavirus VP1 proteins contain conserved RdRp motifs that reside in the catalytic "palm" domain of all classes of polymerases. However, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps. This RdRp has the five essential RNA polymerase motifs in a permuted order of C-A-B-D-E to form a conserved catalytic active site. This domain is mostly alpha-helical that runs across the canyon in the front of the palm, and wraps around the fingers subdomain, which may function to prevent back-primed RNA synthesis during protein priming.
The actual alignment was detected with superfamily member pfam20489:
Pssm-ID: 466638 Cd Length: 103 Bit Score: 135.20 E-value: 2.73e-37
Birnavirus RNA dependent RNA polymerase (VP1), palm domain; Birnaviruses are dsRNA viruses. This entry corresponds to the "palm" domain of the RNA dependent RNA polymerase, also known as VP1. All of the birnavirus VP1 proteins contain conserved RdRp motifs that reside in the catalytic "palm" domain of all classes of polymerases. However, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps. The catalytic motifs are arranged in a permuted order in sequence.
Pssm-ID: 461223 Cd Length: 531 Bit Score: 1000.26 E-value: 0e+00
Birnavirus RNA dependent RNA polymerase (VP1), thumb domain; Birnaviruses are dsRNA viruses. ...
523-687
1.40e-97
Birnavirus RNA dependent RNA polymerase (VP1), thumb domain; Birnaviruses are dsRNA viruses. The RNA dependent RNA polymerase, also known as VP1, contains the conserved RdRp motifs that reside in the catalytic "palm" domain of all classes of polymerases but in a characteriztic permuted order, thus, it adopts a unique active site topology. Additionally, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps. This entry covers the thumb domain of RdRP from Birnaviruses.
Pssm-ID: 466637 Cd Length: 167 Bit Score: 301.44 E-value: 1.40e-97
Birnavirus RNA dependent RNA polymerase (VP1), C-terminal; Birnaviruses are dsRNA viruses. This entry corresponds to the C-terminal domain of RNA dependent RNA polymerase also known as VP1. All of the birnavirus VP1 proteins contain conserved RdRp motifs that reside in the catalytic "palm" domain of all classes of polymerases. However, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps. This RdRp has the five essential RNA polymerase motifs in a permuted order of C-A-B-D-E to form a conserved catalytic active site. This domain is mostly alpha-helical that runs across the canyon in the front of the palm, and wraps around the fingers subdomain, which may function to prevent back-primed RNA synthesis during protein priming.
Pssm-ID: 466638 Cd Length: 103 Bit Score: 135.20 E-value: 2.73e-37
Birnavirus RNA dependent RNA polymerase (VP1), palm domain; Birnaviruses are dsRNA viruses. This entry corresponds to the "palm" domain of the RNA dependent RNA polymerase, also known as VP1. All of the birnavirus VP1 proteins contain conserved RdRp motifs that reside in the catalytic "palm" domain of all classes of polymerases. However, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps. The catalytic motifs are arranged in a permuted order in sequence.
Pssm-ID: 461223 Cd Length: 531 Bit Score: 1000.26 E-value: 0e+00
Birnavirus RNA dependent RNA polymerase (VP1), thumb domain; Birnaviruses are dsRNA viruses. ...
523-687
1.40e-97
Birnavirus RNA dependent RNA polymerase (VP1), thumb domain; Birnaviruses are dsRNA viruses. The RNA dependent RNA polymerase, also known as VP1, contains the conserved RdRp motifs that reside in the catalytic "palm" domain of all classes of polymerases but in a characteriztic permuted order, thus, it adopts a unique active site topology. Additionally, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps. This entry covers the thumb domain of RdRP from Birnaviruses.
Pssm-ID: 466637 Cd Length: 167 Bit Score: 301.44 E-value: 1.40e-97
Birnavirus RNA dependent RNA polymerase (VP1), C-terminal; Birnaviruses are dsRNA viruses. This entry corresponds to the C-terminal domain of RNA dependent RNA polymerase also known as VP1. All of the birnavirus VP1 proteins contain conserved RdRp motifs that reside in the catalytic "palm" domain of all classes of polymerases. However, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps. This RdRp has the five essential RNA polymerase motifs in a permuted order of C-A-B-D-E to form a conserved catalytic active site. This domain is mostly alpha-helical that runs across the canyon in the front of the palm, and wraps around the fingers subdomain, which may function to prevent back-primed RNA synthesis during protein priming.
Pssm-ID: 466638 Cd Length: 103 Bit Score: 135.20 E-value: 2.73e-37
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
181-368
7.17e-03
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase found in many positive strand RNA eukaryotic viruses. Structural studies indicate that these proteins form the "right hand" structure found in all oligonucleotide polymerases, containing thumb, finger and palm domains, and also the additional bridging finger and thumb domains unique to RNA-directed RNA polymerases.
Pssm-ID: 425815 Cd Length: 450 Bit Score: 39.70 E-value: 7.17e-03
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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