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0  structures 411  species 0  interactions 435  sequences 52  architectures

Family: RdRP_2 (PF00978)

Summary: RNA dependent RNA polymerase

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RNA dependent RNA polymerase Provide feedback

This family may represent an RNA dependent RNA polymerase. The family also contains the following proteins: 2A protein from bromoviruses putative RNA dependent RNA polymerase from tobamoviruses Non structural polyprotein from togaviruses

Literature references

  1. Lemm JA, Rice CM; , J Virol 1993;67:1916-1926.: Roles of nonstructural polyproteins and cleavage products in regulating Sindbis virus RNA replication and transcription. PUBMED:8445717 EPMC:8445717

  2. Osman TA, Buck KW; , J Virol 1996;70:6227-6234.: Complete replication in vitro of tobacco mosaic virus RNA by a template-dependent, membrane-bound RNA polymerase. PUBMED:8709249 EPMC:8709249

  3. Dinant S, Janda M, Kroner PA, Ahlquist P; , J Virol 1993;67:7181-7189.: Bromovirus RNA replication and transcription require compatibility between the polymerase- and helicase-like viral RNA synthesis proteins. PUBMED:8230440 EPMC:8230440

  4. Koonin EV, Dolja VV; , Crit Rev Biochem Mol Biol 1993;28:375-430.: Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences. PUBMED:8269709 EPMC:8269709

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001788

This entry represents RNA dependent RNA polymerases found in several types of viruses [ PUBMED:8269709 ], especially those with a tripartite genome (RNA1, RNA2 and RNA3) and an encapsidated subgenomic RNA (RNA4) from which the coat protein is expressed, such as Cucumber mosaic virus (strain NT9) (CMV). This entry contains the following proteins:

  • Viral RNA-directed RNA polymerase 2A (protein 2A) [ PUBMED:15746101 ].
  • Putative RNA dependent RNA polymerase from Tobacco mosaic virus [ PUBMED:8709249 ].
  • Non structural polyprotein from Togavirus [ PUBMED:8445717 ].

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 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 11 members:

Birna_RdRp DUF6451 Flavi_NS5 Mitovir_RNA_pol RdRP_1 RdRP_2 RdRP_3 RdRP_4 RVT_1 RVT_2 Viral_RdRp_C


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 and the UniProtKB 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.

Representative proteomes UniProt
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Representative proteomes UniProt

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

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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...


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_13 (release 3.0)
Previous IDs: RNA_dep_RNApol2;
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD , Bateman A , Griffiths-Jones SR
Number in seed: 36
Number in full: 435
Average length of the domain: 373.60 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 20.12 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.1 21.1
Trusted cut-off 21.1 21.2
Noise cut-off 20.9 21.0
Model length: 440
Family (HMM) version: 23
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence


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