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0  structures 209  species 0  interactions 2070  sequences 413  architectures

Family: HYR (PF02494)

Summary: HYR domain

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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.

HYR domain Provide feedback

This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion [1].

Literature references

  1. Callebaut I, Gilges D, Vigon I, Mornon JP; , Protein Sci 2000;9:1382-1390.: HYR, an extracellular module involved in cellular adhesion and related to the immunoglobulin-like fold. PUBMED:10933504 EPMC:10933504


This tab holds annotation information from the InterPro database.

InterPro entry IPR003410

The HYR (HYalin Repeat) domain is an extracellular domain of about 80-100 amino acids. It has been named after the hyalin protein, which is composed exclusively of repeats of this domain. The HYR domain is found in several eukaryotic proteins, either in multiple copies as in hyalin or in association with other domains like the CCP (sushi) domain, the Von Willebrand factor type A (VWA) domain, the EGF-like domain, the calcium-binding EGF-like domain, the pentraxin domain, the CUB domain, the LDL-receptor class A domain, the C-type lectin domain or the discoidin domain. As the HYR domains of hyalin have been shown to contain the ligand for the hyalin cell surface receptor, the HYR domain can also be expected to play a direct role in cellular adhesion in other proteins in which it is present [PUBMED:10933504].

Secondary structure predictions of the HYR domain indicate an all-beta fold including seven beta-strands. The HYR domain shares clear sequence similarities limited to the C-terminal region with the Fn3 and PKD domains and is believed to belong to the immunoglobulin-like fold [PUBMED:10933504].

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 (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
(13)
Full
(2070)
Representative proteomes UniProt
(3528)
NCBI
(6211)
Meta
(510)
RP15
(1434)
RP35
(1719)
RP55
(2168)
RP75
(2440)
Jalview View  View  View  View  View  View  View  View  View 
HTML View  View               
PP/heatmap 1 View               

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

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

Format an alignment

  Seed
(13)
Full
(2070)
Representative proteomes UniProt
(3528)
NCBI
(6211)
Meta
(510)
RP15
(1434)
RP35
(1719)
RP55
(2168)
RP75
(2440)
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
(13)
Full
(2070)
Representative proteomes UniProt
(3528)
NCBI
(6211)
Meta
(510)
RP15
(1434)
RP35
(1719)
RP55
(2168)
RP75
(2440)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download   Download  

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 View help on the curation process

Seed source: [1]
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 13
Number in full: 2070
Average length of the domain: 80.50 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 15.10 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.2 21.2
Trusted cut-off 21.2 21.2
Noise cut-off 21.1 21.1
Model length: 81
Family (HMM) version: 14
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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