Fig. 1: Overview of components in pcSecYeast.

a Simplified schematic processes involved in the protein secretory pathway. The process includes protein translation, translocation, glycosylate, GPI transfer, ERAD and sorting process. The detailed description of all components and reactions can be found in Supplementary Methods. The protein secretion reactions are added for all proteins in the model that are processed in the secretory pathway based on their PTM profiles and amino acid sequences. Transloc translocation, NG N-glycosylation, OG O-glycosylation, DSB disulfide bond formation, GPI glycosylphosphatidylinositol, ER Endoplasmic reticulum, ERAD ER-associated degradation, LDSV low-density secretory vesicles, HDSV high-density secretory vesicles, ALPP alkaline phosphatase pathway, CPYP carboxypeptidase Y pathway. b Subsystems in the secretory pathway and the protein number in each subsystem. All proteins processed by the secretory pathway are client proteins for Transloc, COPII and ERAD. c Coupling process in the model. The metabolic part produces energy and precursors such as amino acids, glycans for enzyme and ribosome synthesis. Enzymes constrain these metabolic reactions. Ribosomes constrain protein translation. The secretory machinery constrains protein processing in this pathway. All proteins, including ribosomes are diluted due to growth and degraded due to misfolding. Source data are provided as a Source Data file.