Activates the ATG1 kinase in a nutritional condition dependent manner through the TOR pathway, leading to autophagy (By similarity). Involved in ATG9 and ATG23 cycling through the pre-autophagosomal structure (By similarity). Also involved in cytoplasm to vacuole transport (Cvt) and more specifically in Cvt vesicle formation (By similarity). Seems to play a role in the switching machinery regulating the conversion between the Cvt pathway and autophagy (By similarity). Finally, ATG13 is also required for glycogen storage during stationary phase (By similarity). Acts as a negative regulator of xylose alcoholic fermentation, a role that is not related to autophagy (PubMed:29438555). Hypophosphorylated form interacts with ATG1 to form the ATG1-ATG13 kinase complex (By similarity). The ATG1-ATG13 complex interacts with the ATG17-ATG29-ATG31 complex through direct interaction with ATG17. Interacts with VAC8 (By similarity). Leads to derepression of several genes involved in xylose catabolism including PDC1, DAS1 and AOX1, and subsequent increased ethanol production from xylose (PubMed:29438555). Belongs to the ATG13 family. Fungi subfamily.