Summary: Birnavirus RNA dependent RNA polymerase (VP1), C-terminal
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Birnaviridae Edit Wikipedia article
Template:Taxobox begin placement virus
Template:Taxobox group iii entry
Template:Taxobox familia entry
Template:Taxobox end placement
Template:Taxobox section subdivision
Entomobirnavirus Template:Taxobox end The viridae are a family of viruses, including the following genera:
- Genus Aquabirnavirus; type species: Infectious pancreatic necrosis virus
- Genus Avibirnavirus; type species: Infectious bursal disease virus
- Genus Entomobirnavirus; type species: Drosophila X virus
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Birnavirus RNA dependent RNA polymerase (VP1), C-terminal Provide feedback
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 [2,3]. 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.
Shwed PS, Dobos P, Cameron LA, Vakharia VN, Duncan R; , Virology 2002;296:241-250.: Birnavirus VP1 Proteins Form a Distinct Subgroup of RNA-Dependent RNA Polymerases Lacking a GDD Motif. PUBMED:12069523 EPMC:12069523
Pan J, Vakharia VN, Tao YJ;, Proc Natl Acad Sci U S A. 2007;104:7385-7390.: The structure of a birnavirus polymerase reveals a distinct active site topology. PUBMED:17456597 EPMC:17456597
Gorbalenya AE, Pringle FM, Zeddam JL, Luke BT, Cameron CE, Kalmakoff J, Hanzlik TN, Gordon KH, Ward VK;, J Mol Biol. 2002;324:47-62.: The palm subdomain-based active site is internally permuted in viral RNA-dependent RNA polymerases of an ancient lineage. PUBMED:12421558 EPMC:12421558
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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This family is new in this Pfam release.
|Seed source:||Pfam-B_2204 (release 7.3)|
|Number in seed:||3|
|Number in full:||8|
|Average length of the domain:||105.4 aa|
|Average identity of full alignment:||43 %|
|Average coverage of the sequence by the domain:||12.29 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||1|
|Download:||download the raw HMM for this family|
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The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
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Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
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Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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The tree shows the occurrence of this domain across different species. More...
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For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
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Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Birna_RdRp_C domain has been found. There are 29 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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