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47  structures 938  species 3  interactions 1140  sequences 35  architectures

Family: RNA_pol_I_A49 (PF06870)

Summary: A49-like RNA polymerase I associated factor

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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.

A49-like RNA polymerase I associated factor Provide feedback

Saccharomyces cerevisiae A49 is a specific subunit associated with RNA polymerase I (Pol I) in eukaryotes. Pol I maintains transcription activities in A49 deletion mutants. However, such mutants are deficient in transcription activity at low temperatures. Deletion analysis of the fusion yeast homolog indicate that only the C-terminal two thirds are required for function. Transcript analysis has demonstrated that A49 is maximising transcription of ribosomal DNA [1].

Literature references

  1. Nakagawa K, Hisatake K, Imazawa Y, Ishiguro A, Matsumoto M, Pape L, Ishihama A, Nogi Y; , Genes Genet Syst 2003;78:199-209.: The fission yeast RPA51 is a functional homolog of the budding yeast A49 subunit of RNA polymerase I and required for maximizing transcription of ribosomal DNA. PUBMED:12893961 EPMC:12893961


This tab holds annotation information from the InterPro database.

InterPro entry IPR009668

Saccharomyces cerevisiae A49 is a specific subunit associated with RNA polymerase I (Pol I) in eukaryotes. Pol I maintains transcription activities in A49 deletion mutants. However, such mutants are deficient in transcription activity at low temperatures. Deletion analysis of the fusion yeast homologue indicates that only the C-terminal two thirds are required for function. Transcript analysis has demonstrated that A49 is maximising transcription of ribosomal DNA [PUBMED:12893961].

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 Triple_barrel (CL0662), which has the following description:

Members of this superfamily adopt a triple barrel fold. This fold was first identified in the structure of the homodimer of RAP30 and RAP74. The two proteins form a single core structure composed of three interwoven beta barrels [1]. The central barrel is composed of beta strands from both heterodimer subunits. A similar fold has been observed in the heterodimer of TAF1 and TAF7 [2].

The clan contains the following 9 members:

DUF3591 RNA_pol_I_A49 RNA_pol_Rpc4 RNA_polI_A34 RNase_H2_suC Sin_N TAFII55_N TFIIF_beta_N Ydr279_N

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...

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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
(109)
Full
(1140)
Representative proteomes UniProt
(1631)
NCBI
(1838)
Meta
(1)
RP15
(324)
RP35
(639)
RP55
(901)
RP75
(1095)
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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
(109)
Full
(1140)
Representative proteomes UniProt
(1631)
NCBI
(1838)
Meta
(1)
RP15
(324)
RP35
(639)
RP55
(901)
RP75
(1095)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(109)
Full
(1140)
Representative proteomes UniProt
(1631)
NCBI
(1838)
Meta
(1)
RP15
(324)
RP35
(639)
RP55
(901)
RP75
(1095)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   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_20222 (release 10.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD
Number in seed: 109
Number in full: 1140
Average length of the domain: 336.00 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 81.66 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.2 20.2
Trusted cut-off 20.7 20.6
Noise cut-off 19.7 20.1
Model length: 385
Family (HMM) version: 12
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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Interactions

There are 3 interactions for this family. More...

RNA_polI_A34 RNA_polI_A34 RNA_pol_I_A49

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_I_A49 domain has been found. There are 47 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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