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0  structures 262  species 0  interactions 392  sequences 8  architectures

Family: BRE (PF06113)

Summary: Brain and reproductive organ-expressed protein (BRE)

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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.

Brain and reproductive organ-expressed protein (BRE) Provide feedback

This family consists of several eukaryotic brain and reproductive organ-expressed (BRE) proteins. BRE is a putative stress-modulating gene, found able to down-regulate TNF-alpha-induced-NF-kappaB activation upon over expression. A total of six isoforms are produced by alternative splicing predominantly at either end of the gene.Compared to normal cells, immortalised human cell lines uniformly express higher levels of BRE. Peripheral blood monocytes respond to LPS by down-regulating the expression of all the BRE isoforms.It is thought that the function of BRE and its isoforms is to regulate peroxisomal activities [1].

Literature references

  1. Ching AK, Li PS, Li Q, Chan BC, Chan JY, Lim PL, Pang JC, Chui YL; , Biochem Biophys Res Commun 2001;288:535-545.: Expression of human BRE in multiple isoforms. PUBMED:11676476 EPMC:11676476


This tab holds annotation information from the InterPro database.

InterPro entry IPR010358

Brain and reproductive organ-expressed (BRE, also known as BRCC45) is a component of the BRCA1-A complex, a complex that specifically recognises 'Lys-63'-linked ubiquitinated histones H2A and H2AX at DNA lesions sites, leading to target the BRCA1-BARD1 heterodimer to sites of DNA damage at double-strand breaks (DSBs) [PUBMED:14636569]. It acts as an adapter that bridges the interaction between BABAM1/NBA1 and the rest of the complex, thereby being required for the complex integrity and modulating the E3 ubiquitin ligase activity of the BRCA1-BARD1 heterodimer [PUBMED:21282113, PUBMED:19261748]. It is also part of the BRISC complex, a multiprotein complex that specifically cleaves 'Lys-63'-linked ubiquitin in various substrates [PUBMED:19214193, PUBMED:24075985, PUBMED:25283148, PUBMED:26195665]. Within the BRISC complex, it acts as an adapter that bridges the interaction between BABAM1/NBA1 and the rest of the complex, thereby being required for the complex integrity [PUBMED:21282113].

Gene Ontology

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Domain organisation

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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
(6)
Full
(392)
Representative proteomes UniProt
(583)
NCBI
(893)
Meta
(0)
RP15
(99)
RP35
(203)
RP55
(294)
RP75
(334)
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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
(6)
Full
(392)
Representative proteomes UniProt
(583)
NCBI
(893)
Meta
(0)
RP15
(99)
RP35
(203)
RP55
(294)
RP75
(334)
Alignment:
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Sequence:
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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
(6)
Full
(392)
Representative proteomes UniProt
(583)
NCBI
(893)
Meta
(0)
RP15
(99)
RP35
(203)
RP55
(294)
RP75
(334)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download    
Gzipped 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: Pfam-B_9280 (release 9.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Moxon SJ
Number in seed: 6
Number in full: 392
Average length of the domain: 271.40 aa
Average identity of full alignment: 37 %
Average coverage of the sequence by the domain: 78.74 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.8 25.8
Trusted cut-off 26.0 26.6
Noise cut-off 25.3 25.7
Model length: 320
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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