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0  structures 30  species 0  interactions 226  sequences 34  architectures

Family: Peptidase_S31 (PF05578)

Summary: Pestivirus NS3 polyprotein peptidase S31

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.

Pestivirus NS3 polyprotein peptidase S31 Provide feedback

These serine peptidases are involved in processing of the flavivirus polyprotein.

Literature references

  1. Ryan MD, Monaghan S, Flint M; , J Gen Virol 1998;79:947-959.: Virus-encoded proteinases of the Flaviviridae. PUBMED:9603310 EPMC:9603310


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000280

The genome of pestiviruses is a single plus-strand RNA and contains a single large open reading frame (ORF), a 5' untranslated region (5'UTR) and a 3' untranslated region (3'UTR). The ORF encodes a polyprotein, which is processed by viral and cellular proteases into mature proteins (the structural proteins in the N-terminal portion of the polyprotein whilst the replicative (non-structural or NS) proteins constitute the remainder).

The pestivirus NS3 protein is a multifunctional protein possessing serine protease, RNA helicase, and a nucleoside triphosphatase (NTPase) activities located in two functionally distinct domains. The N-terminal one-third of pestiviral NS3 primarily serves as a protease to process the viral polyprotein. The helicase and NTPase activities are localized to the C- terminal of NS3 protein [PUBMED:2543956, PUBMED:9603310, PUBMED:19951725]. The NS3 protease domain has approximately 180 aa with a catalytic triad of His-Asp-Ser. Positive regulation (activation) is observed by its interaction with NS4A. The pestivirus NS3 proteolytic domain constitutes MEROPS peptidase family S31 of clan PA.

This entry represents the pestivirus NS3 protease domain.

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 Peptidase_PA (CL0124), which has the following description:

This clan contains a diverse set of peptidases with the trypsin fold.

The clan contains the following 24 members:

DUF1986 DUF31 DUF316 Peptidase_C24 Peptidase_C3 Peptidase_C30 Peptidase_C37 Peptidase_C3G Peptidase_C4 Peptidase_C62 Peptidase_S29 Peptidase_S3 Peptidase_S30 Peptidase_S31 Peptidase_S32 Peptidase_S39 Peptidase_S46 Peptidase_S55 Peptidase_S6 Peptidase_S7 Peptidase_S76 Pico_P2A Trypsin Trypsin_2

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
(4)
Full
(226)
Representative proteomes NCBI
(244)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
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HTML View  View             
PP/heatmap 1 View             
Pfam viewer View  View             

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(4)
Full
(226)
Representative proteomes NCBI
(244)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
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
(4)
Full
(226)
Representative proteomes NCBI
(244)
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: Merops
Previous IDs: none
Type: Family
Author: Studholme DJ
Number in seed: 4
Number in full: 226
Average length of the domain: 175.10 aa
Average identity of full alignment: 90 %
Average coverage of the sequence by the domain: 7.31 %

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 20.5 20.5
Trusted cut-off 22.6 25.0
Noise cut-off 20.4 18.5
Model length: 211
Family (HMM) version: 7
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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