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36  structures 1800  species 0  interactions 3154  sequences 58  architectures

Family: RNA_pol (PF00940)

Summary: DNA-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.

This is the Wikipedia entry entitled "T7 RNA polymerase". More...

T7 RNA polymerase Edit Wikipedia article

T7 RNA Polymerase is an RNA polymerase that catalyzes the formation of RNA in the 5'-3' direction. T7 RNA polymerase also requires the presence of a T7 promoter on the DNA sequence to be transcribed. The source of the enzyme is the T7 bacteriophate, which is a virus that infects only bacteria. It has a molecular weight of 99 kDa.

==External Links==

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

DNA-dependent RNA polymerase Provide feedback

This is a family of single chain RNA polymerases.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002092

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 700kDa, contain two non-identical large (>100kDa) subunits and an array of up to 12 different small (less than 50kDa) subunits.

The phage-type enzymes are family of single chain polymerases found in bacteriophages and mitochondria [ PUBMED:7526118 ].

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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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 and the UniProtKB 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
(190)
Full
(3154)
Representative proteomes UniProt
(5901)
RP15
(943)
RP35
(1711)
RP55
(2592)
RP75
(3312)
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PP/heatmap 1 View           

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

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

Format an alignment

  Seed
(190)
Full
(3154)
Representative proteomes UniProt
(5901)
RP15
(943)
RP35
(1711)
RP55
(2592)
RP75
(3312)
Alignment:
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Sequence:
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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
(190)
Full
(3154)
Representative proteomes UniProt
(5901)
RP15
(943)
RP35
(1711)
RP55
(2592)
RP75
(3312)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   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.

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_1108 (release 3.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD , Bateman A
Number in seed: 190
Number in full: 3154
Average length of the domain: 385.8 aa
Average identity of full alignment: 41 %
Average coverage of the sequence by the domain: 39.7 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.0 22.0
Trusted cut-off 22.2 22.2
Noise cut-off 21.5 21.8
Model length: 426
Family (HMM) version: 22
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

Selections

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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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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 RNA_pol domain has been found. There are 36 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A044VE71 View 3D Structure Click here
A0A077ZFJ4 View 3D Structure Click here
A0A0D2HBC4 View 3D Structure Click here
A0A0K0ECF8 View 3D Structure Click here
A0A0R0EEG8 View 3D Structure Click here
A0A0R0FNB7 View 3D Structure Click here
A0A0R0ISI6 View 3D Structure Click here
A0A0R0KED1 View 3D Structure Click here
A0A0R4ILV6 View 3D Structure Click here
A0A175VP72 View 3D Structure Click here
A0A1C1C7E7 View 3D Structure Click here
A0A1D6GPN4 View 3D Structure Click here
A0A1D6IJV3 View 3D Structure Click here
A0A1D6IUV6 View 3D Structure Click here
A0A1D6KEL6 View 3D Structure Click here
A0A1D6L678 View 3D Structure Click here
A0A1D6LG76 View 3D Structure Click here
A0A1D6N946 View 3D Structure Click here
A0A1D6NX96 View 3D Structure Click here
A0A1D6P567 View 3D Structure Click here
A0A1D8PCA4 View 3D Structure Click here
A0A1D8PR19 View 3D Structure Click here
A0A3P7FE93 View 3D Structure Click here
A0A3P7Q9B2 View 3D Structure Click here
A0A3Q0KPI7 View 3D Structure Click here
A4I0V3 View 3D Structure Click here
A5PEY3 View 3D Structure Click here
C0NPG4 View 3D Structure Click here
C1GZG1 View 3D Structure Click here
D3ZYB6 View 3D Structure Click here
I1JWD0 View 3D Structure Click here
I1MT00 View 3D Structure Click here
K7K9S6 View 3D Structure Click here
K7KWI1 View 3D Structure Click here
K7L8Z9 View 3D Structure Click here
K7L904 View 3D Structure Click here
K7MG43 View 3D Structure Click here
K7MV39 View 3D Structure Click here
O00411 View 3D Structure Click here
O13993 View 3D Structure Click here