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41  structures 1281  species 0  interactions 2211  sequences 70  architectures

Family: ATG16 (PF08614)

Summary: Autophagy protein 16 (ATG16)

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.

Autophagy protein 16 (ATG16) Provide feedback

Autophagy is a ubiquitous intracellular degradation system for eukaryotic cells. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. ATG16 (also known as Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate in the yeast autophagy pathway [1].

Literature references

  1. Mizushima N, Noda T, Ohsumi Y; , EMBO J. 1999;18:3888-3896.: Apg16p is required for the function of the Apg12p-Apg5p conjugate in the yeast autophagy pathway. PUBMED:10406794 EPMC:10406794

  2. Matsushita M, Suzuki NN, Fujioka Y, Ohsumi Y, Inagaki F; , Acta Crystallograph Sect F Struct Biol Cryst Commun. 2006;62:1021-1023.: Expression, purification and crystallization of the Atg5-Atg16 complex essential for autophagy. PUBMED:17012802 EPMC:17012802


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013923

Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Atg proteins coordinate the formation of autophagosomes. The pre-autophagosomal structure contains at least five Atg proteins: Atg1p, Atg2p, Atg5p, Aut7p/Atg8p and Atg16p. It is found in the vacuole [ PUBMED:11689437 , PUBMED:2306415 ]. The C-terminal glycine of Atg12p is conjugated to a lysine residue of Atg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Autophagy protein 16 (Atg16) has been shown to be bind to Atg5 and is required for the function of the Atg12p-Atg5p conjugate [ PUBMED:10406794 ]. Autophagy protein 5 (Atg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway [ PUBMED:10712513 ].

This entry represents autophagy protein 16 (Apg16), which is required for the function of the Apg12p-Apg5p conjugate.

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
(101)
Full
(2211)
Representative proteomes UniProt
(3399)
RP15
(314)
RP35
(791)
RP55
(1587)
RP75
(2247)
Jalview View  View  View  View  View  View  View 
HTML View  View           
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
(101)
Full
(2211)
Representative proteomes UniProt
(3399)
RP15
(314)
RP35
(791)
RP55
(1587)
RP75
(2247)
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
(101)
Full
(2211)
Representative proteomes UniProt
(3399)
RP15
(314)
RP35
(791)
RP55
(1587)
RP75
(2247)
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: manual
Previous IDs: none
Type: Coiled-coil
Sequence Ontology: SO:0001080
Author: Mistry J , Wood V
Number in seed: 101
Number in full: 2211
Average length of the domain: 175.1 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 38.85 %

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 33.7 33.7
Trusted cut-off 33.7 33.7
Noise cut-off 33.6 33.6
Model length: 201
Family (HMM) version: 14
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 ATG16 domain has been found. There are 41 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
A0A044SLS0 View 3D Structure Click here
A0A077YXF2 View 3D Structure Click here
A0A0D2H589 View 3D Structure Click here
A0A0G2K9U6 View 3D Structure Click here
A0A0R4IBY0 View 3D Structure Click here
A0A175W5A5 View 3D Structure Click here
A0A1C1C905 View 3D Structure Click here
A0A3P7DPP1 View 3D Structure Click here
A0A3P7PVJ9 View 3D Structure Click here
A0A7I4KHM6 View 3D Structure Click here
A0A7I4KJZ5 View 3D Structure Click here
A5DIB1 View 3D Structure Click here
A7TIN2 View 3D Structure Click here
B7Z0R7 View 3D Structure Click here
C0NFP1 View 3D Structure Click here
C0PGH8 View 3D Structure Click here
C1GUY6 View 3D Structure Click here
D4A9M7 View 3D Structure Click here
I1K068 View 3D Structure Click here
I1MUK8 View 3D Structure Click here
I1RFS8 View 3D Structure Click here
O15736 View 3D Structure Click here
Q03818 View 3D Structure Click here
Q10CZ9 View 3D Structure Click here
Q19124 View 3D Structure Click here
Q4WVH5 View 3D Structure Click here
Q520U5 View 3D Structure Click here
Q5BH90 View 3D Structure Click here
Q5I0B9 View 3D Structure Click here
Q5RAC9 View 3D Structure Click here
Q676U5 View 3D Structure Click here
Q6BH63 View 3D Structure Click here
Q6C4Y4 View 3D Structure Click here
Q6CPX2 View 3D Structure Click here
Q6FJ38 View 3D Structure Click here
Q6KAU8 View 3D Structure Click here
Q6NNP0 View 3D Structure Click here
Q755K3 View 3D Structure Click here
Q8C0J2 View 3D Structure Click here
Q8NAA4 View 3D Structure Click here