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0  structures 40  species 0  interactions 45  sequences 1  architecture

Family: Chordopox_RPO7 (PF05864)

Summary: Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7)

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Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7) Provide feedback

This family consists of several Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide sequences. DNA-dependent RNA polymerase catalyses the transcription of DNA into RNA.

Literature references

  1. Amegadzie BY, Ahn BY, Moss B; , J Virol 1992;66:3003-3010.: Characterization of a 7-kilodalton subunit of vaccinia virus DNA-dependent RNA polymerase with structural similarities to the smallest subunit of eukaryotic RNA polymerase II. PUBMED:1560534 EPMC:1560534


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008448

DNA-directed RNA polymerases EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme [PUBMED:3052291]. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length [PUBMED:10499798]. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.

RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:

  • RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs.
  • RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors.
  • RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs.
Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits.

This family consists of several Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide sequences. DNA-dependent RNA polymerase catalyses the transcription of DNA into RNA [PUBMED:1560534].

Gene Ontology

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

Domain organisation

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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...

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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
(7)
Full
(45)
Representative proteomes NCBI
(20)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(7)
Full
(45)
Representative proteomes NCBI
(20)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
Alignment:
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Sequence:
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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
(7)
Full
(45)
Representative proteomes NCBI
(20)
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.

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

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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_9596 (release 8.0)
Previous IDs: none
Type: Family
Author: Moxon SJ
Number in seed: 7
Number in full: 45
Average length of the domain: 63.00 aa
Average identity of full alignment: 78 %
Average coverage of the sequence by the domain: 99.96 %

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 25.6 25.6
Trusted cut-off 25.7 107.0
Noise cut-off 25.5 25.5
Model length: 63
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

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