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2  structures 47  species 0  interactions 257  sequences 7  architectures

Family: Peptidase_C9 (PF01707)

Summary: Peptidase family C9

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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.

Peptidase family C9 Provide feedback

No Pfam abstract.

Literature references

  1. Rumenapf T, Strauss EG, Strauss JH; , Virology 1995;208:621-633.: Aura virus is a New World representative of Sindbis-like viruses. PUBMED:7747434 EPMC:7747434


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002620

The family of alphaviruses includes 26 known members. They infect a variety of hosts including mosquitoes, birds, rodents and other mammals with worldwide distribution. Alphaviruses also pose a potential threat to human health in many area. For example, Venezuelan Equine Encephalitis Virus (VEEV) causes encephalitis in humans as well as livestock in Central and South America, and some variants of Sinbis Virus (SIN) and Semliki Forest Virus (SFV) have been found to cause fever and arthritis in humans [PUBMED:19013248].

Alphaviruses possess a single-stranded RNA genome of approximately 12 kb. The genomic RNA of alphaviruses is translated into two polyproteins that, respectively, encode structural proteins and nonstructural proteins. The nonstructural proteins may be translated as one or two polyproteins, nsp123 or nsp1234, depending on the virus. These polyproteins are cleaved to generate nsp1, nsp2, nsp3 and nsp4 by a protease activity that resides within nsp2 [PUBMED:11257180]. The nsp2 protein of alphaviruses has multiple enzymatic acivities. Its N-terminal domain has been shown to possess ATPase and GTPase activity, RNA helicase activity and RNA 5'-triphosphatase activity [PUBMED:10748213]. The C-terminal nsp2pro domain of nsp2 is responsible for the regulation of 26S subgenome RNA synthesis, switching between negative- and positive-strand RNA synthesis, targeting nsp2 for nuclear transport and proteolytic processing of the nonstructural polyprotein [PUBMED:19013248, PUBMED:16962975]. The nsp2pro domain is a member of peptidase family C9 of clan CA.

The nsp2pro domain consists of two distinct subdomains. The nsp2pro N-terminal subdomain is largely alpha-helical and contains the catalytic dyad cysteine and histidine residues organised in a protein fold that differs significantly from any known cysteine protease or protein folds. The nsp2pro C-terminal subdomain displays structural similarity to S-adenosyl- L-methionine-dependent RNA methyltransferases and provides essential elements that contribute to substrate recognition and may also regulate the structure of the substrate binding cleft [PUBMED:16962975].

This entry represents the nsp2pro domain.

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(8)
Full
(257)
Representative proteomes NCBI
(311)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
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PP/heatmap 1 View             
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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
(8)
Full
(257)
Representative proteomes NCBI
(311)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
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
(8)
Full
(257)
Representative proteomes NCBI
(311)
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.

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: [1]
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 8
Number in full: 257
Average length of the domain: 192.80 aa
Average identity of full alignment: 66 %
Average coverage of the sequence by the domain: 8.58 %

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 25.0 25.0
Trusted cut-off 115.5 114.6
Noise cut-off 22.3 20.0
Model length: 202
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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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 Peptidase_C9 domain has been found. There are 2 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 seqence.

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