Activates the atg1 kinase in a nutritional condition dependent manner through the TOR pathway, leading to autophagy. Also involved in cytoplasm to vacuole transport (Cvt) and more specifically in Cvt vesicle formation. Seems to play a role in the switching machinery regulating the conversion between the Cvt pathway and autophagy. Finally, atg13 is also required for glycogen storage during stationary phase (By similarity). Interacts with atg1 to form the atg1-atg13 kinase complex. Belongs to the ATG13 family. Fungi subfamily.