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Family: Viral_RdRp_C (PF17501)

Summary: Viral RNA-directed RNA polymerase

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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Viral RNA-directed RNA polymerase Provide feedback

This is the C-terminal of RNA-directed RNA polymerase (Protein A) found in Alphanodaviruses such as Flock House Virus (FHV). FHV is a positive-stranded RNA virus with a bipartite genome of RNAs, RNA1 and RNA2. RNA1 encodes protein A, which is the catalytic subunit of the RNA-dependent RNA polymerase (RdRp) [1] and functions as the sole viral replicase protein responsible for RNA replication. FHV protein A also possesses a terminal nucleotidyl transferase (TNTase) activity, which is able to restore the nucleotide loss at the 3′-end initiation site of RNA template to rescue RNA synthesis initiation. It has also been reported that FHV protein A replicates viral RNA in concert with the mitochondrial outer membrane and other viral or cellular factors and mediates the formation of viral RNA replication complexes and small spherules by inducing membrane rearrangement [2].This domain is also found in B1 proteins which are encoded by the subgenomic RNA3 during FHV replication. The function of translated B1 protein is poorly defined, but may be important for maintenance of RNA replication [3].

Literature references

  1. Liu Y, Zhao Y, Zhang Y, Chen H;, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013;69:1147-1150.: Crystallization and preliminary crystallographic analysis of a viral RNA-silencing suppressor encoded by Wuhan nodavirus. PUBMED:24100569 EPMC:24100569

  2. Wu W, Wang Z, Xia H, Liu Y, Qiu Y, Liu Y, Hu Y, Zhou X;, PLoS One. 2014;9:e86876.: Flock house virus RNA polymerase initiates RNA synthesis de novo and possesses a terminal nucleotidyl transferase activity. PUBMED:24466277 EPMC:24466277

  3. Maharaj PD, Mallajosyula JK, Lee G, Thi P, Zhou Y, Kearney CM, McCormick AA;, Int J Mol Sci. 2014;15:18540-18556.: Nanoparticle encapsidation of Flock house virus by auto assembly of Tobacco mosaic virus coat protein. PUBMED:25318056 EPMC:25318056


This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan RdRP (CL0027), which has the following description:

This clan represents the replicative RNA dependent RNA polymerase. from a variety of RNA viruses [1].

The clan contains the following 10 members:

Birna_RdRp Flavi_NS5 Mitovir_RNA_pol RdRP_1 RdRP_2 RdRP_3 RdRP_4 RVT_1 RVT_2 Viral_RdRp_C

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(4)
Full
(0)
Representative proteomes UniProt
(18)
NCBI
(15)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
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PP/heatmap 1                

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(4)
Full
(0)
Representative proteomes UniProt
(18)
NCBI
(15)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
Alignment:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(4)
Full
(0)
Representative proteomes UniProt
(18)
NCBI
(15)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
Raw Stockholm Download             Download   Download    
Gzipped Download             Download   Download    

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

This family is new in this Pfam release.

Seed source: PRODOM:PD029982
Previous IDs: none
Type: Family
Author: El-Gebali S
Number in seed: 4
Number in full: 0
Average length of the domain: 0.00 aa
Average identity of full alignment: 0 %
Average coverage of the sequence by the domain: 0.00 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 102.3 101.5
Noise cut-off 22.1 21.2
Model length: 101
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

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