Summary: Autophagy-related protein 13
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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
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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
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Tsukada M, Ohsumi Y; , FEBS Lett. 1993;333:169-174.: Isolation and characterization of autophagy-defective mutants of Saccharomyces cerevisiae. PUBMED:8224160 EPMC:8224160
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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.
Cellular component | Atg1/ULK1 kinase complex (GO:1990316) |
Biological process | autophagy (GO:0006914) |
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
Alignments
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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 (98) |
Full (2340) |
Representative proteomes | UniProt (3583) |
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RP15 (354) |
RP35 (979) |
RP55 (1773) |
RP75 (2414) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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Seed (98) |
Full (2340) |
Representative proteomes | UniProt (3583) |
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RP15 (354) |
RP35 (979) |
RP55 (1773) |
RP75 (2414) |
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Raw Stockholm | |||||||
Gzipped |
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.
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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
Seed source: | KOGs (KOG4573) |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
KOGs, Finn RD |
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
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 239 | ||||||||||||
Family (HMM) version: | 12 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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.