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108  structures 8145  species 2  interactions 9404  sequences 15  architectures

Family: Calici_coat (PF00915)

Summary: Calicivirus coat protein

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Calicivirus coat protein Provide feedback

No Pfam abstract.

Literature references

  1. Meyers G, Wirblich C, Thiel H-J; , Virology 1991;184:664-676.: Rabbit hemorrhagic disease virus--molecular cloning and nucleotide sequencing of a calicivirus genome. PUBMED:1840711 EPMC:1840711


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004005

Bovine calicivirus is a positive-stranded ssRNA viruses that cause gastroenteritis [PUBMED:1840711]. The calicivirus genome contains two open reading frames, ORF1 and ORF2 [PUBMED:8892921, PUBMED:8642693]. ORF1 encodes a non-structural polypeptide, which has RNA helicase, cysteine protease and RNA polymerase activity. The regions of the poly-protein in which these activities lie are similar to proteins produced by the picornaviruses [PUBMED:8892921, PUBMED:1551442]. ORF2 encodes a structural protein [PUBMED:8892921]. This signature finds ORF2, the structural coat protein. Two different families of caliciviruses can be distinguished on the basis of sequence similarity, namely those classified as small round structured viruses (SRSVs) and those classed as non-SRSVs.

Rabbit hemorrhagic disease virus (RHDV) which causes a highly contagious disease of wild and domestic rabbits belongs to the family Caliciviridae [PUBMED:16733562]. The capsid protein self assembles to form an icosahedral capsid with a T=3 symmetry. It is about 38nm in diameter and consists of 180 capsid proteins. The capsid encapsulates the genomic RNA and VP2 proteins and attaches the virion to target cells by binding histo-blood group antigens present on gastroduodenal epithelial cells. The Shell domain (S domain) contains elements essential for the formation of the icosahedron. The Protruding domain (P domain) is divided into sub-domains P1 and P2. An hypervariable region in P2 is thought to play an important role in receptor binding and immune reactivity.

This entry includes the Calicivirus coat protein as well as the non-structural polyprotein.

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 Viral_ssRNA_CP (CL0055), which has the following description:

The clan contains a set of viral coat protein families and peptidase A6. The only known peptidase activity is an autolytic cleavage releasing a 44-residue C-terminal fragment. The reaction is very slow and only occurs within the assembled virion. There is debate whether this is actually a true peptidase. The virion with these coat or capsid proteins are icosahedral viruses containing sixty triangular coat protein units, each unit consisting of three proteins. The coat protein consists of two subdomains, an eight-stranded beta-barrel on the surface and a three-helix bundle on the inner face.

The clan contains the following 17 members:

Birna_VP2 Bromo_coat Calici_coat Capsid-VNN Circo_capsid Como_LCP CRPV_capsid Cucumo_coat Luteo_coat Nepo_coat Peptidase_A21 Peptidase_A6 Rhv SP2 TT_ORF1 Tymo_coat Viral_coat

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
(11)
Full
(9404)
Representative proteomes NCBI
(7359)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
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PP/heatmap 1              
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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
(11)
Full
(9404)
Representative proteomes NCBI
(7359)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(11)
Full
(9404)
Representative proteomes NCBI
(7359)
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: Pfam-B_202 (release 3.0)
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 11
Number in full: 9404
Average length of the domain: 130.20 aa
Average identity of full alignment: 53 %
Average coverage of the sequence by the domain: 60.76 %

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 19.9 19.9
Trusted cut-off 19.9 19.9
Noise cut-off 19.8 19.8
Model length: 293
Family (HMM) version: 15
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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Interactions

There are 2 interactions for this family. More...

Calici_coat Calici_coat_C

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 Calici_coat domain has been found. There are 108 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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