Summary: RNA polymerase Rpb1, domain 7
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RNA polymerase Rpb1, domain 7 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 7, represents a mobile module of the RNA polymerase. Domain 7 forms a substantial interaction with the lobe domain of Rpb2 (PF04561) [1,2].
Literature references
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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
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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
SCOOP: | RNA_pol_Rpb1_5 |
Similarity to PfamA using HHSearch: | RNA_pol_Rpb1_5 |
External database links
SCOP: | 1i50 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR007073
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 7, represents a mobile module of the RNA polymerase. Domain 7 interacts with the lobe domain of Rpb2 (INTERPRO) [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.
Molecular function | DNA-directed 5'-3' RNA polymerase activity (GO:0003899) |
DNA binding (GO:0003677) | |
Biological process | transcription, DNA-templated (GO:0006351) |
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, the UniProtKB sequence database, 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 (72) |
Full (1474) |
Representative proteomes | UniProt (3448) |
NCBI (3446) |
Meta (167) |
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RP15 (303) |
RP35 (689) |
RP55 (1108) |
RP75 (1492) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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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 (72) |
Full (1474) |
Representative proteomes | UniProt (3448) |
NCBI (3446) |
Meta (167) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (303) |
RP35 (689) |
RP55 (1108) |
RP75 (1492) |
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Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | Pfam-B_288 (release 4.2) |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Finn RD |
Number in seed: | 72 |
Number in full: | 1474 |
Average length of the domain: | 131.20 aa |
Average identity of full alignment: | 47 % |
Average coverage of the sequence by the domain: | 7.95 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 135 | ||||||||||||
Family (HMM) version: | 13 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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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Interactions
There are 6 interactions for this family. More...
RNA_pol_Rpb1_5 RNA_pol_Rpb1_4 RNA_pol_Rpb5_N TFIIS_M RNA_POL_M_15KD RNA_pol_Rpb2_2Structures
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_7 domain has been found. There are 174 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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