Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
796  structures 8710  species 0  interactions 15393  sequences 433  architectures

Family: RNA_pol_Rpb1_5 (PF04998)

Summary: RNA polymerase Rpb1, domain 5

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.

RNA polymerase Rpb1, domain 5 Provide feedback

RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound [1,2].

Literature references

  1. Severinov K, Mustaev A, Kukarin A, Muzzin O, Bass I, Darst SA, Goldfarb A; , J Biol Chem 1996;271:27969-27974.: Structural modules of the large subunits of RNA polymerase. Introducing archaebacterial and chloroplast split sites in the beta and beta' subunits of Escherichia coli RNA polymerase. PUBMED:8910400 EPMC:8910400

  2. Cramer P, Bushnell DA, Kornberg RD; , Science 2001;292:1863-1876.: Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. PUBMED:11313498 EPMC:11313498


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007081

RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to form the central cleft or channel where the DNA is bound [ PUBMED:8910400 , PUBMED:11313498 ].

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...

Loading domain graphics...

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
(24)
Full
(15393)
Representative proteomes UniProt
(80021)
RP15
(2895)
RP35
(7834)
RP55
(14262)
RP75
(22056)
Jalview View  View  View  View  View  View  View 
HTML View             
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
(24)
Full
(15393)
Representative proteomes UniProt
(80021)
RP15
(2895)
RP35
(7834)
RP55
(14262)
RP75
(22056)
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
(24)
Full
(15393)
Representative proteomes UniProt
(80021)
RP15
(2895)
RP35
(7834)
RP55
(14262)
RP75
(22056)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped 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: Manual
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
Number in seed: 24
Number in full: 15393
Average length of the domain: 463.00 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 35.83 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 28.5 28.5
Trusted cut-off 28.5 28.5
Noise cut-off 28.4 28.4
Model length: 267
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

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

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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_Rpb1_5 domain has been found. There are 796 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.

Loading structure mapping...

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
A0A0P0WI29 View 3D Structure Click here
A0A0R0G598 View 3D Structure Click here
A0A0R0GY74 View 3D Structure Click here
A0A0R0L5S8 View 3D Structure Click here
A0A0R4I9V4 View 3D Structure Click here
A0A0R4IMS9 View 3D Structure Click here
A0A0R4IV41 View 3D Structure Click here
A0A1D6E7H3 View 3D Structure Click here
A0A1D6K232 View 3D Structure Click here
A0A1D6KIY2 View 3D Structure Click here
A0A1D6LLQ3 View 3D Structure Click here
A0A1D6QSZ1 View 3D Structure Click here
A0A1D8PEX3 View 3D Structure Click here
A0A1D8PMS1 View 3D Structure Click here
A0A1D8PUA6 View 3D Structure Click here
A0A1X7YHF8 View 3D Structure Click here
A0A5K1K9C5 View 3D Structure Click here
A4HX31 View 3D Structure Click here
A4I766 View 3D Structure Click here
A4I9K6 View 3D Structure Click here
A8JUY3 View 3D Structure Click here
B2RXC6 View 3D Structure Click here
D4A5A6 View 3D Structure Click here
E9PTB6 View 3D Structure Click here
F4JXF9 View 3D Structure Click here
G5ED21 View 3D Structure Click here
I1L748 View 3D Structure Click here
I1L9X1 View 3D Structure Click here
I1LK95 View 3D Structure Click here
K7K465 View 3D Structure Click here
K7LNL8 View 3D Structure Click here
K7TLU2 View 3D Structure Click here
O14802 View 3D Structure Click here
O35134 View 3D Structure Click here
O54889 View 3D Structure Click here
O77375 View 3D Structure Click here
O94666 View 3D Structure Click here
O95602 View 3D Structure Click here
P04050 View 3D Structure Click here
P04051 View 3D Structure Click here
P04052 View 3D Structure Click here
P08775 View 3D Structure Click here
P0A8T7 View 3D Structure Click here
P0C509 View 3D Structure Click here
P0C509 View 3D Structure Click here
P10964 View 3D Structure Click here
P15398 View 3D Structure Click here
P16025 View 3D Structure Click here
P16025 View 3D Structure Click here
P16356 View 3D Structure Click here
P18616 View 3D Structure Click here
P24928 View 3D Structure Click here
P35084 View 3D Structure Click here
P36594 View 3D Structure Click here
P56764 View 3D Structure Click here
P56764 View 3D Structure Click here
P91875 View 3D Structure Click here
P9WGY7 View 3D Structure Click here
Q0DAZ6 View 3D Structure Click here
Q18566 View 3D Structure Click here
Q25802 View 3D Structure Click here
Q2G0N5 View 3D Structure Click here
Q4CKJ3 View 3D Structure Click here
Q4CKK7 View 3D Structure Click here
Q4CPY8 View 3D Structure Click here
Q4D133 View 3D Structure Click here
Q4D483 View 3D Structure Click here
Q4DDX5 View 3D Structure Click here
Q4DZA9 View 3D Structure Click here
Q58445 View 3D Structure Click here
Q58446 View 3D Structure Click here
Q58446 View 3D Structure Click here
Q5D869 View 3D Structure Click here
Q7X881 View 3D Structure Click here
Q86AQ5 View 3D Structure Click here
Q86H36 View 3D Structure Click here
Q8HVY3 View 3D Structure Click here
Q8HVY3 View 3D Structure Click here
Q8IE49 View 3D Structure Click here
Q8IE49 View 3D Structure Click here
Q9SVY0 View 3D Structure Click here