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116  structures 1662  species 0  interactions 11412  sequences 209  architectures

Family: Sec63 (PF02889)

Summary: Sec63 Brl domain

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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.

Sec63 Brl domain Provide feedback

This domain (also known as the Brl domain) is required for assembly of functional endoplasmic reticulum translocons [2].

Literature references

  1. Ponting CP; , Biochem J 2000;351:527-535.: Proteins of the endoplasmic-reticulum-associated degradation pathway: domain detection and function prediction. PUBMED:11023840 EPMC:11023840

  2. Jermy AJ, Willer M, Davis E, Wilkinson BM, Stirling CJ; , J Biol Chem. 2006;281:7899-7906.: The Brl domain in Sec63p is required for assembly of functional endoplasmic reticulum translocons. PUBMED:16368690 EPMC:16368690


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004179

This domain was named after the yeast Sec63 (or NPL1) (also known as the Brl domain) protein in which it was found. This protein is required for assembly of functional endoplasmic reticulum translocons [ PUBMED:16368690 , PUBMED:11023840 ]. Other yeast proteins containing this domain include pre-mRNA splicing helicase BRR2, HFM1 protein and putative helicases.

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
(84)
Full
(11412)
Representative proteomes UniProt
(19154)
RP15
(2318)
RP35
(5151)
RP55
(8886)
RP75
(11776)
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
(84)
Full
(11412)
Representative proteomes UniProt
(19154)
RP15
(2318)
RP35
(5151)
RP55
(8886)
RP75
(11776)
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
(84)
Full
(11412)
Representative proteomes UniProt
(19154)
RP15
(2318)
RP35
(5151)
RP55
(8886)
RP75
(11776)
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: Ponting CP
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 84
Number in full: 11412
Average length of the domain: 288.8 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 31.37 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 25.0 25.0
Noise cut-off 24.9 24.9
Model length: 259
Family (HMM) version: 19
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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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 Sec63 domain has been found. There are 116 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
A0A044QSY4 View 3D Structure Click here
A0A044R7T5 View 3D Structure Click here
A0A077Z5M4 View 3D Structure Click here
A0A077Z5Y2 View 3D Structure Click here
A0A077ZHI7 View 3D Structure Click here
A0A0D2G7K8 View 3D Structure Click here
A0A0D2GWW7 View 3D Structure Click here
A0A0D2H8F9 View 3D Structure Click here
A0A0G2JUJ9 View 3D Structure Click here
A0A0H5S2Y0 View 3D Structure Click here
A0A0K0DSB7 View 3D Structure Click here
A0A0K0DSL9 View 3D Structure Click here
A0A0K0E0R5 View 3D Structure Click here
A0A0K0IZ06 View 3D Structure Click here
A0A0N4UEL0 View 3D Structure Click here
A0A0N4UHR6 View 3D Structure Click here
A0A0P0VDW4 View 3D Structure Click here
A0A0P0VUU2 View 3D Structure Click here
A0A0R0FWV1 View 3D Structure Click here
A0A0R4IN50 View 3D Structure Click here
A0A175VYP9 View 3D Structure Click here
A0A175W858 View 3D Structure Click here
A0A175WJM2 View 3D Structure Click here
A0A1C1CI77 View 3D Structure Click here
A0A1C1CQX8 View 3D Structure Click here
A0A1C1D2M4 View 3D Structure Click here
A0A1D6EDJ2 View 3D Structure Click here
A0A1D6IKW3 View 3D Structure Click here
A0A1D6J573 View 3D Structure Click here
A0A1D6LUX1 View 3D Structure Click here
A0A1D6PH86 View 3D Structure Click here
A0A1D6Q526 View 3D Structure Click here
A0A1D8PH33 View 3D Structure Click here
A0A1D8PMR5 View 3D Structure Click here
A0A1D8PP41 View 3D Structure Click here
A0A1U7F4E3 View 3D Structure Click here
A0A2K6WMM3 View 3D Structure Click here
A0A3P7E965 View 3D Structure Click here
A0A3P7EAQ1 View 3D Structure Click here
A0A3P7PS66 View 3D Structure Click here