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228  structures 263  species 1  interaction 17276  sequences 48  architectures

Family: RdRP_3 (PF00998)

Summary: Viral RNA dependent RNA polymerase

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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 dependent RNA polymerase Provide feedback

This family includes viral RNA dependent RNA polymerase enzymes from hepatitis C virus and various plant viruses.

Literature references

  1. Lohmann V, Korner F, Herian U, Bartenschlager R; , J Virol 1997;71:8416-8428.: Biochemical properties of hepatitis C virus NS5B RNA-dependent RNA polymerase and identification of amino acid sequence motifs essential for enzymatic activity. PUBMED:9343198 EPMC:9343198

  2. Behrens SE, Tomei L, De Francesco R; , EMBO J 1996;15:12-22.: Identification and properties of the RNA-dependent RNA polymerase of hepatitis C virus. PUBMED:8598194 EPMC:8598194

  3. Ishido S, Fujita T, Hotta H; , Biochem Biophys Res Commun 1998;244:35-40.: Complex formation of NS5B with NS3 and NS4A proteins of hepatitis C virus. PUBMED:9514871 EPMC:9514871


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002166

The RNA dependent RNA polymerase is also known as non-structural protein NS5B. NS5B is a 65 kDa protein that resembles other viral RNA polymerases. Hepatitis C virus (HCV) replication is thought to occur in membrane bound replication complexes. These complexes transcribe the positive strand and the resulting minus strand is used as a template for the synthesis of genomic RNA. There are two viral proteins involved in the reaction, NS3 and NS5B [PUBMED:9343198, PUBMED:8598194, PUBMED:9514871].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 contains the following 8 members:

Flavi_NS5 Mitovir_RNA_pol RdRP_1 RdRP_2 RdRP_3 RdRP_4 RVT_1 RVT_2

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

View options

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
(33)
Full
(17276)
Representative proteomes NCBI
(13782)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(1)
RP75
(1)
Jalview View  View      View  View  View   
HTML View        View  View     
PP/heatmap 1       View  View     
Pfam viewer View  View             

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

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

Format an alignment

  Seed
(33)
Full
(17276)
Representative proteomes NCBI
(13782)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(1)
RP75
(1)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(33)
Full
(17276)
Representative proteomes NCBI
(13782)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(1)
RP75
(1)
Raw Stockholm Download   Download       Download   Download   Download    
Gzipped Download   Download       Download   Download   Download    

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

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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

Seed source: Pfam-B_315 (release 3.0)
Previous IDs: HCV_RdRP; Viral_RdRP;
Type: Family
Author: Finn RD, Bateman A, Griffiths-Jones SR
Number in seed: 33
Number in full: 17276
Average length of the domain: 190.90 aa
Average identity of full alignment: 62 %
Average coverage of the sequence by the domain: 44.48 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 19.6 19.6
Trusted cut-off 19.6 19.6
Noise cut-off 19.5 19.5
Model length: 486
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

Sunburst controls

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Tree controls

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Interactions

There is 1 interaction for this family. More...

RdRP_3

Structures

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 RdRP_3 domain has been found. There are 228 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 seqence.

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