Summary: Ilarvirus coat protein
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Ilarvirus coat protein Provide feedback
This family consists of various coat proteins from the ilarviruses part of the Bromoviridae, members include apple mosaic virus and prune dwarf virus. The ilarvirus coat protein is required to initiate replication of the viral genome in host plants [1]. Members of the Bromoviridae have a positive stand ssRNA genome with no DNA stage in there replication.
Literature references
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Guo D, Maiss E, Adam G, Casper R; , J Gen Virol 1995;76:1073-1079.: Prunus necrotic ringspot ilarvirus: nucleotide sequence of RNA3 and the relationship to other ilarviruses based on coat protein comparison. PUBMED:7730792 EPMC:7730792
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Bachman EJ, Scott SW, Xin G, Vance VB; , Virology 1994;201:127-131.: The complete nucleotide sequence of prune dwarf ilarvirus RNA 3: implications for coat protein activation of genome replication in ilarviruses. PUBMED:8178476 EPMC:8178476
This tab holds annotation information from the InterPro database.
InterPro entry IPR002681
This family consists of various coat proteins from the Ilarviruses which belong to the Bromoviridae, members include Apple mosaic virus and Prune dwarf virus. The Ilarvirus coat protein is required to initiate replication of the viral genome in host plants [PUBMED:7730792]. Members of the Bromoviridae have a positive stand ssRNA genome with no DNA stage in their replication.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Cellular component | virion (GO:0019012) |
Molecular function | RNA binding (GO:0003723) |
Biological process | translational initiation (GO:0006413) |
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 Nucleoplasmin (CL0055), which has the following description:
This large superfamily includes nucleoplasmin as well as a wide range of viral coat and capsid proteins that share a jelly roll topology.
The clan contains the following 42 members:
Adeno_hexon_C Astro_capsid_N Birna_VP2 Bromo_coat Calici_coat Calici_coat_C Capsid-VNN Capsid_N Carmo_coat_C Circo_capsid Como_LCP Como_SCP CRPV_capsid Cucumo_coat Dicistro_VP4 DUF2961 DUF4621 HAV_VP IHHNV_capsid Ilar_coat Late_protein_L1 Luteo_coat Nepo_coat Nepo_coat_C Nepo_coat_N NPL Nucleoplasmin Peptidase_A21 Peptidase_A6 Pico_P1A Polyhedrin Polyoma_coat Pox_Rif Rhv SP2 TGFb_propeptide TNV_CP TT_ORF1 Tymo_coat Viral_coat VP4_2 Waikav_capsid_1Alignments
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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, 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 (20) |
Full (15) |
Representative proteomes | UniProt (988) |
NCBI (951) |
Meta (0) |
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RP15 (17) |
RP35 (17) |
RP55 (17) |
RP75 (17) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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not generated,
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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 (20) |
Full (15) |
Representative proteomes | UniProt (988) |
NCBI (951) |
Meta (0) |
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RP15 (17) |
RP35 (17) |
RP55 (17) |
RP75 (17) |
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Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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
Seed source: | Pfam-B_1131 (release 4.2) |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Bashton M |
Number in seed: | 20 |
Number in full: | 15 |
Average length of the domain: | 202.90 aa |
Average identity of full alignment: | 21 % |
Average coverage of the sequence by the domain: | 91.38 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 204 | ||||||||||||
Family (HMM) version: | 17 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Selections
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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 is 1 interaction for this family. More...
Ilar_coatStructures
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 Ilar_coat domain has been found. There are 11 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 sequence.
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