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19  structures 1258  species 0  interactions 2340  sequences 20  architectures

Family: ATG13 (PF10033)

Summary: Autophagy-related protein 13

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-related protein 13 Provide feedback

Members of this family of phosphoproteins are involved in cytoplasm to vacuole transport (Cvt), and more specifically in Cvt vesicle formation. They are probably involved in the switching machinery regulating the conversion between the Cvt pathway and autophagy. Finally, ATG13 is also required for glycogen storage [1].

Literature references

  1. Funakoshi T, Matsuura A, Noda T, Ohsumi Y; , Gene. 1997;192:207-213.: Analyses of APG13 gene involved in autophagy in yeast, Saccharomyces cerevisiae. PUBMED:9224892 EPMC:9224892

  2. Tsukada M, Ohsumi Y; , FEBS Lett. 1993;333:169-174.: Isolation and characterization of autophagy-defective mutants of Saccharomyces cerevisiae. PUBMED:8224160 EPMC:8224160

  3. Scott SV, Nice DC 3rd, Nau JJ, Weisman LS, Kamada Y, Keizer-Gunnink I, Funakoshi T, Veenhuis M, Ohsumi Y, Klionsky DJ; , J Biol Chem. 2000;275:25840-25849.: Apg13p and Vac8p are part of a complex of phosphoproteins that are required for cytoplasm to vacuole targeting. PUBMED:10837477 EPMC:10837477


This tab holds annotation information from the InterPro database.

InterPro entry IPR018731

This entry represents the N-terminal domain of autophagy-related protein 13 (Atg13) from yeasts, animals and plants. They function in autophagy.

Fission yeast autophagy initiation is controlled by the Atg1 kinase complex, which is composed of the Ser/Thr kinase Atg1, the adaptor protein Atg13, and the ternary complex of Atg17-Atg31-Atg29. Atg13 recruits Atg1 to the site of autophagosome formation and enhancing Atg1 kinase activity. Atg13 may have additional functions that are independent of a direct interaction or permanent colocalization with Atg1 [ PUBMED:24879146 ].

In vertebrates, the orthologous ULK1 kinase complex contains the Ser/Thr kinase ULK1 and the accessory proteins ATG13, RB1CC1, and ATG101 [ PUBMED:24879146 ]. Through its regulation of ULK1 activity, Atg13 plays a role in the regulation of the kinase activity of mTORC1 and cell proliferation [ PUBMED:19225151 ].

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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Pfam Clan

This family is a member of clan Mad2 (CL0651), which has the following description:

The clan contains the following 5 members:

ATG101 ATG13 bacHORMA_2 HORMA p31comet

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
(98)
Full
(2340)
Representative proteomes UniProt
(3583)
RP15
(354)
RP35
(979)
RP55
(1773)
RP75
(2414)
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
(98)
Full
(2340)
Representative proteomes UniProt
(3583)
RP15
(354)
RP35
(979)
RP55
(1773)
RP75
(2414)
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
(98)
Full
(2340)
Representative proteomes UniProt
(3583)
RP15
(354)
RP35
(979)
RP55
(1773)
RP75
(2414)
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: KOGs (KOG4573)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: KOGs, Finn RD , Sammut SJ
Number in seed: 98
Number in full: 2340
Average length of the domain: 170.9 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 27.89 %

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 25.0 25.0
Trusted cut-off 25.1 25.0
Noise cut-off 24.9 24.9
Model length: 239
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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Colour assignments

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 ATG13 domain has been found. There are 19 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
A0A0D2F0R4 View 3D Structure Click here
A0A0K0E9Y1 View 3D Structure Click here
A0A0P0XZM3 View 3D Structure Click here
A0A175VPZ6 View 3D Structure Click here
A0A1C1CD15 View 3D Structure Click here
A0A1D6EHT8 View 3D Structure Click here
A0A1D6HEP4 View 3D Structure Click here
A2QWA6 View 3D Structure Click here
A3LQY1 View 3D Structure Click here
A4IIM9 View 3D Structure Click here
A5A6N3 View 3D Structure Click here
A5DQA8 View 3D Structure Click here
A7F7B2 View 3D Structure Click here
A7KAM4 View 3D Structure Click here
A7TTE2 View 3D Structure Click here
C0NS26 View 3D Structure Click here
C1GRW0 View 3D Structure Click here
C4IZF6 View 3D Structure Click here
D3ZA45 View 3D Structure Click here
F4J8V5 View 3D Structure Click here
I1JH67 View 3D Structure Click here
I1K4W4 View 3D Structure Click here
I1RW37 View 3D Structure Click here
K7L6R5 View 3D Structure Click here
K7M7X6 View 3D Structure Click here
K7TMF5 View 3D Structure Click here
K7UHG9 View 3D Structure Click here
K7UPK8 View 3D Structure Click here
O36019 View 3D Structure Click here
O75143 View 3D Structure Click here
Q06628 View 3D Structure Click here
Q08DY8 View 3D Structure Click here
Q0JBE1 View 3D Structure Click here
Q0UPX4 View 3D Structure Click here
Q1E891 View 3D Structure Click here
Q2ULT1 View 3D Structure Click here
Q4WHN5 View 3D Structure Click here
Q55BY0 View 3D Structure Click here
Q5A1Z5 View 3D Structure Click here
Q5BBK4 View 3D Structure Click here