Activates the ATG1 kinase in a nutritional condition dependent manner through the TOR pathway, leading to autophagy (PubMed:10995454, PubMed:11086004, PubMed:15743910, PubMed:17295840, PubMed:18077553, PubMed:18287526, PubMed:19805182, PubMed:19995911, PubMed:20647741, PubMed:20855505, PubMed:22447937, PubMed:22778255, PubMed:22782902, PubMed:22885598, PubMed:8224160, PubMed:21468027). Required for autophosphorylation of ATG1 at 'Thr-226' and its dimerization (PubMed:20439775, PubMed:17699586, PubMed:21712380). May also be involved in the regulation of autophagy through SNF1 (PubMed:11486014). Involved in ATG9 and ATG23 cycling through the pre-autophagosomal structure (PubMed:14723849, PubMed:17426440). Also involved in cytoplasm to vacuole transport (Cvt) and more specifically in Cvt vesicle formation (PubMed:10837477). Seems to play a role in the switching machinery regulating the conversion between the Cvt pathway and autophagy (PubMed:10837477). Finally, ATG13 is also required for glycogen storage during stationary phase (PubMed:11486014). Hypophosphorylated form interacts with ATG1 to form the ATG1-ATG13 kinase complex (PubMed:10995454, PubMed:15743910, PubMed:15901835, PubMed:18829864, PubMed:20439775, PubMed:20953146, PubMed:21712380, PubMed:22778255, PubMed:22885598). The ATG1-ATG13 complex interacts with the ATG17-ATG29-ATG31 complex through direct interaction with ATG17 (PubMed:23219485, PubMed:15743910, PubMed:15901835, PubMed:19755117, PubMed:19805182). Interacts with VAC8 (PubMed:10837477). Phosphorylated; hyperphosphorylated by the TORC1 kinase complex to repress the induction of autophagy in nutrient-replete conditions (PubMed:10995454, PubMed:19995911, PubMed:19805182, PubMed:22447937, PubMed:22727621, PubMed:29698392). Starvation and TOR inactivation results in ATG13 partial dephosphorylation leading to ATG1-binding (PubMed:10995454). Rephosphorylated by ATG1 during prolonged nitrogen starvation (PubMed:21490424). Also phosphorylated by PKA (PubMed:17699586, PubMed:19805182, PubMed:21078689). PKA phosphorylation regulates the association of ATG13 with the PAS (PubMed:21900499). Within this regulatory network, mitochondrial respiratory deficiency suppresses autophagic flux (PubMed:21468027). Hyperphosphorylation in rich medium is impaired in the absence of VAC8 (PubMed:10837477). Dephosphorylation is dependent on FAR11 (PubMed:22782902). Present with 149 molecules/cell in log phase SD medium. Belongs to the ATG13 family. Fungi subfamily.