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6  structures 1493  species 0  interactions 9688  sequences 347  architectures

Family: Beach (PF02138)

Summary: Beige/BEACH domain

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.

Beige/BEACH domain Provide feedback

No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000409

The BEACH domain is usually followed by a series of WD repeats.

BEACH (Beige and Chediak-Higashi) domains, implicated in membrane trafficking, are present in a family of proteins conserved throughout eukaryotes. This group contains human lysosomal trafficking regulator (LYST), LPS-responsive and beige-like anchor (LRBA) and neurobeachin. Disruption of LYST leads to Chediak-Higashi syndrome, characterized by severe immunodeficiency, albinism, poor blood coagulation and neurologic problems. Neurobeachin is a candidate gene linked to autism. LBRA seems to be upregulated in several cancer types. It has been shown that the BEACH domain itself is important for the function of these proteins [ PUBMED:17079274 , PUBMED:15086784 , PUBMED:12125812 , PUBMED:15342963 , PUBMED:15193433 , PUBMED:11102458 , PUBMED:12535270 , PUBMED:12210762 ].

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 and the UniProtKB 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
(271)
Full
(9688)
Representative proteomes UniProt
(15588)
RP15
(1787)
RP35
(3704)
RP55
(7379)
RP75
(9916)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

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

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

Format an alignment

  Seed
(271)
Full
(9688)
Representative proteomes UniProt
(15588)
RP15
(1787)
RP35
(3704)
RP55
(7379)
RP75
(9916)
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
(271)
Full
(9688)
Representative proteomes UniProt
(15588)
RP15
(1787)
RP35
(3704)
RP55
(7379)
RP75
(9916)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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: IPR000409
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Mian N , Bateman A
Number in seed: 271
Number in full: 9688
Average length of the domain: 256.80 aa
Average identity of full alignment: 49 %
Average coverage of the sequence by the domain: 11.18 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.8 26.8
Trusted cut-off 26.9 26.9
Noise cut-off 26.6 26.7
Model length: 274
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

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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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 Beach domain has been found. There are 6 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0G2K4H2 View 3D Structure Click here
A0A0P0V1T8 View 3D Structure Click here
A0A0P0VF72 View 3D Structure Click here
A0A0P0VMT1 View 3D Structure Click here
A0A0P0X088 View 3D Structure Click here
A0A0R4IVV3 View 3D Structure Click here
A0A1D6EHP3 View 3D Structure Click here
A0A1D6EP40 View 3D Structure Click here
A0A1D6K7M2 View 3D Structure Click here
A0A1D6LBM0 View 3D Structure Click here
A0A1D6LPM1 View 3D Structure Click here
A0A1D6MSD1 View 3D Structure Click here
A0A1D6PT25 View 3D Structure Click here
A0A1D6QSN4 View 3D Structure Click here
A0A1D8PDU1 View 3D Structure Click here
A0A2R8RXW6 View 3D Structure Click here
A8XSV3 View 3D Structure Click here
D4A929 View 3D Structure Click here
E7FEV0 View 3D Structure Click here
E9AH19 View 3D Structure Click here
E9PYP2 View 3D Structure Click here
E9QFZ1 View 3D Structure Click here
F1M6V0 View 3D Structure Click here
F1QZ06 View 3D Structure Click here
F4I9T0 View 3D Structure Click here
F4JD14 View 3D Structure Click here
F4JY12 View 3D Structure Click here
K7LL70 View 3D Structure Click here
K7N3K0 View 3D Structure Click here
O35242 View 3D Structure Click here
P25356 View 3D Structure Click here
Q10122 View 3D Structure Click here
Q19317 View 3D Structure Click here
Q4CMM6 View 3D Structure Click here
Q4CXP0 View 3D Structure Click here
Q4D6T0 View 3D Structure Click here
Q4D8V3 View 3D Structure Click here
Q54PP7 View 3D Structure Click here
Q54RQ8 View 3D Structure Click here
Q54U63 View 3D Structure Click here