Summary: BRO1-like 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.
BRO1-like domain Provide feedback
This domain is found in a number proteins including Rhophilin Q61085 and BRO1 P48582. It is known to have a role in endosomal targeting. ESCRT-III subunit Snf7 binds to a conserved hydrophobic patch in the BRO1 domain that is required for protein complex formation and for the protein-sorting function of BRO1 [2].
Literature references
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Toyooka S, Ouchida M, Jitsumori Y, Tsukuda K, Sakai A, Nakamura A, Shimizu N, Shimizu K; , Biochem Biophys Res Commun 2000;278:671-678.: HD-PTP: A novel protein tyrosine phosphatase gene on human chromosome 3p21.3. PUBMED:11095967 EPMC:11095967
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Kim J, Sitaraman S, Hierro A, Beach BM, Odorizzi G, Hurley JH; , Dev Cell 2005;8:937-947.: Structural basis for endosomal targeting by the Bro1 domain. PUBMED:15935782 EPMC:15935782
Internal database links
SCOOP: | DUF5355 SRP68 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR004328
The BRO1 domain is a protein domain of ~390 residues in length. It occurs in a number of eukaryotic proteins, such as yeast BRO1 and human PDCD6IP/Alix, which are involved in protein targeting to the vacuole or lysosome. The BRO1 domain of fungal and mammalian proteins binds with multivesicular body components (ESCRT-III proteins) such as yeast Snf7 and mammalian CHMP4b, and can function to target BRO1 domain-containing proteins to endosomes [PUBMED:15935782, PUBMED:14583093, PUBMED:15944343].
The BRO1 domain has a boomerang shape composed of 14 alpha-helices and 3 beta-sheets. It contains a TPR-like substructure in the central part [PUBMED:15935782]. The C terminus is less conserved.
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...
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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 (201) |
Full (4382) |
Representative proteomes | UniProt (7231) |
NCBI (9691) |
Meta (8) |
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RP15 (764) |
RP35 (2075) |
RP55 (3306) |
RP75 (4496) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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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 (201) |
Full (4382) |
Representative proteomes | UniProt (7231) |
NCBI (9691) |
Meta (8) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (764) |
RP35 (2075) |
RP55 (3306) |
RP75 (4496) |
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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: | Bateman A |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Bateman A |
Number in seed: | 201 |
Number in full: | 4382 |
Average length of the domain: | 344.80 aa |
Average identity of full alignment: | 23 % |
Average coverage of the sequence by the domain: | 45.84 % |
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: | 386 | ||||||||||||
Family (HMM) version: | 19 | ||||||||||||
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
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 BRO1 domain has been found. There are 64 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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