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10  structures 951  species 1  interaction 1306  sequences 24  architectures

Family: APG6 (PF04111)

Summary: Apg6 BARA 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.

Apg6 BARA domain Provide feedback

In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells [1]. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway [2]. This entry is the Beta-Alpha repeated, autophagy-specific (BARA) domain [3].

Literature references

  1. Suzuki K, Kirisako T, Kamada Y, Mizushima N, Noda T, Ohsumi Y; , EMBO J 2001;20:5971-5981.: The pre-autophagosomal structure organized by concerted functions of APG genes is essential for autophagosome formation. PUBMED:11689437 EPMC:11689437

  2. Kametaka S, Okano T, Ohsumi M, Ohsumi Y; , J Biol Chem 1998;273:22284-22291.: Apg14p and Apg6/Vps30p form a protein complex essential for autophagy in the yeast, Saccharomyces cerevisiae. PUBMED:9712845 EPMC:9712845

  3. Noda NN, Kobayashi T, Adachi W, Fujioka Y, Ohsumi Y, Inagaki F;, J Biol Chem. 2012;287:16256-16266.: Structure of the novel C-terminal domain of vacuolar protein sorting 30/autophagy-related protein 6 and its specific role in autophagy. PUBMED:22437838 EPMC:22437838


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007243

In yeasts, vacuolar protein sorting-associated protein 30 (Vps30), also known as autophagy-related protein 6 (Atg6), is a common component of two distinct phosphatidylinositol 3-kinase complexes. In complex I, Atg14 links Vps30 to Vps34 lipid kinase and plays a specific role in autophagy, while in complex II, Vps38 links Vps30 to Vps34 and plays an important role in vacuolar protein sorting [PUBMED:22437838]. The C-terminal of Vps30 contains a globular fold comprised of three beta-sheet-alpha-helix repeats and is required for autophagy through the targeting of complex I to the pre-autophagosomal structure. The N-terminal of Vps30 is required for vacuolar protein sorting [PUBMED:22437838].

Beclin 1, the mammalian homologue of yeast Atg6/Vps30, is a tumour suppressor that coordinately regulates the autophagy and membrane trafficking involved in several physiological and pathological processes [PUBMED:21311563, PUBMED:22170155].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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
(128)
Full
(1306)
Representative proteomes UniProt
(1900)
NCBI
(2270)
Meta
(4)
RP15
(356)
RP35
(699)
RP55
(985)
RP75
(1207)
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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
(128)
Full
(1306)
Representative proteomes UniProt
(1900)
NCBI
(2270)
Meta
(4)
RP15
(356)
RP35
(699)
RP55
(985)
RP75
(1207)
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
(128)
Full
(1306)
Representative proteomes UniProt
(1900)
NCBI
(2270)
Meta
(4)
RP15
(356)
RP35
(699)
RP55
(985)
RP75
(1207)
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: Pfam-B_11747 (release 7.3);
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Wood V , Finn RD , Bateman A
Number in seed: 128
Number in full: 1306
Average length of the domain: 173.90 aa
Average identity of full alignment: 43 %
Average coverage of the sequence by the domain: 37.46 %

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 34.0 34.0
Trusted cut-off 34.0 34.0
Noise cut-off 33.5 33.7
Model length: 179
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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Interactions

There is 1 interaction for this family. More...

APG6

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 APG6 domain has been found. There are 10 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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