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. Autophagy functions to supply nitrogen and is activated when cells cannot access exogenous nitrogen, thus ensuring that they can adapt and subsequently propagate. Finally, atg13 is also required for glycogen storage during stationary phase and has a role in meiosis and sporulation. Interacts with atg1 to form the atg1-atg13 kinase complex. Phosphorylated. Dephosphorylated under depletion of nitrogen. Impairs atg8-processing. Belongs to the ATG13 family. Fungi subfamily.