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0  structures 14  species 0  interactions 524  sequences 17  architectures

Family: Peptidase_C33 (PF05412)

Summary: Equine arterivirus Nsp2-type cysteine proteinase

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Equine arterivirus Nsp2-type cysteine proteinase Provide feedback

Corresponds to Merops family C33. These peptidases are involved in viral polyprotein processing in replication.

Literature references

  1. Ziebuhr J, Snijder EJ, Gorbalenya AE; , J Gen Virol 2000;81:853-879.: Virus-encoded proteinases and proteolytic processing in the Nidovirales. PUBMED:10725411 EPMC:10725411


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008743

Arteriviruses are enveloped, positive-stranded RNA viruses and include pathogens of major economic concern to the swine- and horse-breeding industries:

  • Equine arteritis virus (EAV).
  • Porcine reproductive and respiratory syndrome virus (PRRSV).
  • Mice actate dehydrogenase-elevating virus.
  • Simian hemorrhagic fever virus.

The arterivirus cysteine protease (AV CP) is the most carboxyl-terminally located member of the array of three cysteine proteinase domains present in the amino-terminal 500 residues of the replicase polyproteins. The AV CP is located in the amino-terminal region of nsp2 and is highly conserved among arteriviruses. The cleavage of the nsp2|3 junction appears to be the single processing step mediated by the AV CP. For EAV, it has been shown that cleaved nsp2 is an essential co-factor for cleavage of the nsp4|6 site by the nsp4 proteinase domain. The AV CP is an unusual Cys protease with amino acid sequence similarities to both papain-like and chymotrypsin-like proteases. The catalytic dyad is composed of Cys and His residues [PUBMED:7622476, PUBMED:9371590, PUBMED:10725411]. The AV CP domain forms MEROPS peptidase family C33.

The entire AV CP domain is highly conserved among arteriviruses. Among the conserved residues are a number of cysteines and one aspartate residues [PUBMED:10725411].

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(4)
Full
(524)
Representative proteomes NCBI
(536)
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
(4)
Full
(524)
Representative proteomes NCBI
(536)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
Alignment:
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Sequence:
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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
(4)
Full
(524)
Representative proteomes NCBI
(536)
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: Manual
Previous IDs: none
Type: Family
Author: Studholme DJ
Number in seed: 4
Number in full: 524
Average length of the domain: 105.90 aa
Average identity of full alignment: 66 %
Average coverage of the sequence by the domain: 6.01 %

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 29.3 39.2
Noise cut-off 19.9 17.3
Model length: 108
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

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