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0  structures 2  species 0  interactions 13  sequences 3  architectures

Family: Peptidase_C62 (PF12380)

Summary: Gill-associated viral 3C-like peptidase

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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.

Gill-associated viral 3C-like peptidase Provide feedback

a positive-stranded RNA virus of prawns, that has been called yellow head virus protease and gill-associated virus 3C-like peptidase. The GAV cysteine protease is predicted to be the key enzyme in the processing of the GAV replicase polyprotein precursors, pp1a and pp1ab. This protease employs a Cys(2968)-His(2879) catalytic dyad.

Literature references

  1. Ziebuhr J, Bayer S, Cowley JA, Gorbalenya AE;, J Virol. 2003;77:1415-1426.: The 3C-like proteinase of an invertebrate nidovirus links coronavirus and potyvirus homologs. PUBMED:12502857 EPMC:12502857


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR024348

This protease is found in polyproteins from the positive-stranded RNA virus of prawns called yellow head virus or gill-associated virus (GAV). The GAV cysteine proteinase (3C-like proteinase) is predicted to be the key enzyme in the processing of the GAV replicase polyprotein precursors, polyprotein 1a and polyprotein 1ab. This protease employs a Cys(2968)-His(2879) catalytic dyad [PUBMED:12502857]. It is classified as family C62 in the MEROPS database.

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
(2)
Full
(13)
Representative proteomes NCBI
(15)
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
(2)
Full
(13)
Representative proteomes NCBI
(15)
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
(2)
Full
(13)
Representative proteomes NCBI
(15)
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.

Pfam alignments:

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_C62.001
Previous IDs: none
Type: Family
Author: Coggill P
Number in seed: 2
Number in full: 13
Average length of the domain: 284.00 aa
Average identity of full alignment: 95 %
Average coverage of the sequence by the domain: 6.70 %

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 18.8 18.8
Trusted cut-off 19.6 643.9
Noise cut-off 18.2 18.7
Model length: 284
Family (HMM) version: 3
Download: download the raw HMM for this family

Species distribution

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