Table 2. Characteristics of available models for Phaeodactylum tricornutum.
| Property | Kroth et al. [69] | DiatomCyc [45] | Hunt et al. [71] | Kim et al. [72] | iLB1027_lipid (this study) |
|---|---|---|---|---|---|
| Reactions | 88 | 1719 metabolic reactions 67 transport reactions | 318 | 849 (not including biomass equation) | 4456 (iLB1025: 2156) |
| Metabolites | Not available | 1173 | 335 | 587 | 2172 (iLB1025: 1704) |
| Genes | 151 | 1613 | 680 | 607 | 1027 (iLB1025: 1025) |
| Compartments | Cytoplasm, Mitochondria, Chloroplast, Endoplasmic reticulum, Peroxisome | Cytoplasm | Cytoplasm, Mitochondria, Chloroplast, Peroxisome | Cytoplasm, Mitochondria, Chloroplast (stroma and lumen), Peroxisome | Cytoplasm, Mitochondria, Chloroplast (stroma and thylakoid), Peroxisome |
| Reconstruction software | Not available | Pathway Tools | CellNetAnalyzer | MOST | COBRA Toolbox, COBRApy |
| Availability | No mathematical model available | Online access | SBML | SBML | SBML, MAT |
| Notes | Carbohydrate metabolism | Genome-wide model, not compartmentalized | Simplified and compartmentalized version of DiatomCyc; see [70] for simulations | Genome-wide model, GPRs not in Boolean format | Genome-wide model, detailed lipid metabolism |
Metabolic model characteristics are compared between four available models for P. tricornutum and the one presented in this study.