Table 3. Reactions added based on Pathway Tools analysis.
| Gene | Annotated Gene Function | New HF Gene Function | Hole EC# | Ptools HF Probability | Additional Citation/Rationale |
| MGA_0008 | Putative Glycerol-3-phosphate acyltransferase | Glycerol-3-phosphate O-acyltransferase | 2.3.1.15 | 0.98 | Needed for glycerol incorporation for phospholipid biosynthesis |
| MGA_0161 | Dihydrolipoamide dehydrogenase (E3) component of PDH complex | Glycine Decarboxylase | None | 1.00 | Folate interconversion |
| MGA_0161 | Dihydrolipoamide dehydrogenase (E3) component of PDH complex | NAD(P)(+) Transhydrogenase (B-specific) | 1.6.1.1 | 0.99 | Needed for NADP charging |
| MGA_0181 | Fatty acid/phospholipid synthesis protein Plsx | Acyl-Phosphate Synthase | None | 0.99 | Needed to provide an acyl carrier protein for lipid metabolism |
| MGA_0291 | Inorganic polyphosphate/ATP-NAD kinase | NADH Kinase | 2.7.1.86 | 0.96 | Needed for NADH metabolism |
| MGA_0364 | Purine nucleoside phosphorylase deoD-type | Deoxyinosine phosphatase | None | 0.99 | [109] |
| MGA_0594 | Glutamyl-tRNA synthetase (Glutamate—tRNA ligase) (GluRS) | Glutamine tRNA ligase | 6.1.1.18 | 1.00 | Necessary tRNA charging pathway |
| MGA_0594 | Glutamyl-tRNA synthetase (Glutamate—tRNA ligase) (GluRS) | Glutamine tRNA ligase | None | 0.92 | Necessary to the glutaminyl-tRNA charging pathway |
| MGA_0596 | Bifunctional protein folD | Methylenetetrahydrofolate dehydrogenase (NAD+) | 1.5.1.15 | 1.00 | Homology to Escherichia coli's FolD which catalyzes this reaction |
| MGA_0833 | Acetyl-CoA hydrolase | Acetate CoA transferase | 2.8.3.8 | 0.98 | [105] |
| MGA_0950 | Guanosine polyphosphate pyrophosphohydrolases/synthetase | GTP-pyrophosphokinase | 2.7.6.5 | 1.00 | Needed for ppGpp Biosynthesis |
| MGA_1065 | Asparaginyl-tRNA synthetase | Asparate tRNA ligase | 6.1.1.- | 1.00 | Needed for L-asparginyl tRNA charging pathway |
This table shows the genes, previously annotated functions, newly annotated functions, reaction EC numbers, and HF probability and the rationale for why they were added. All EC numbers were determined via Pathway Tools v14. It should be noted that the functionalities listed here are in addition to the original functionality of the given gene.