Table 3. Stoichiometric inconsistencies in iKF1028 [70].
Reaction: the reaction identifiers in the GEM; Equation: the reaction equations; H left/right: the total number of H atoms at the left/right side of the equations; H residue: the differences between the number of H atoms at the left versus the right side of the equations. Two reactions, RR08939 and IR01815, are shown at the bottom of the table, which correspond to the balanced version of the inconsistent reactions RR00610 and IR04287, respectively. Both pairs (marked with * and **, respectively) were present in iKF1028, rendering the overall model stoichiometrically inconsistent.
| Reaction | Equation | H left | H right | H residue | |
|---|---|---|---|---|---|
| Unbalanced reactions | IR00136 | [c]: 2-Oxoglutarate --> Succinate semialdehyde + CO2 | 4 | 5 | -1 |
| IR00159 | [c]: H2O + Acetyl phosphate --> Orthophosphate + Acetate | 5 | 4 | 1 | |
| IR00373 | [c]: L-Ornithine --> CO2 + Putrescine | 13 | 14 | -1 | |
| IR00765 | [c]: NADP+ + H2O + L-Valine --> NH3 + NADPH + 3-Methyl-2-oxobutanoate | 38 | 36 | 2 | |
| IR01585 | [c]: D-Glucose 6-phosphate + UDPglucose --> alpha,alpha'-Trehalose 6-phosphate + UDP | 33 | 32 | 1 | |
| IR04287** | [c]: Uroporphyrinogen III + (2) S-Adenosyl-L-methionine --> Precorrin 2 + (2) S-Adenosyl-L-homocysteine + H+ | 82 | 89 | -7 | |
| IR04586 | [c]: NADH + NH3 + H+ + Pyruvate --> L-Alanine + H2O + NAD+ | 34 | 35 | -1 | |
| IR09357 | [c]: (S)-3-Hydroxy-3-methylglutaryl-CoA --> Acetyl-CoA + Acetoacetate + (5) H+ | 39 | 44 | -5 | |
| IR10056 | [c]: Precorrin 2 + S-Adenosyl-L-methionine --> Precorrin 3A + S-Adenosyl-L-homocysteine + H+ | 71 | 64 | 7 | |
| IR10481 | [c]: Aminoimidazole ribotide + HCO3- + ATP --> 5-Carboxyamino-1-(5-phospho-D-ribosyl)imidazole + ADP + Orthophosphate | 25 | 27 | -2 | |
| RR00067 | [c]: NAD+ + (2) L-Glutamate <==> L-Glutamine + NADH + 2-Oxoglutarate | 42 | 41 | 1 | |
| RR00610* | [c]: D-Glucose 1-phosphate + (2) H+ <==> D-Glucose 6-phosphate | 13 | 11 | 2 | |
| RR00692 | [c]: D-Fructose 1,6-bisphosphate <==> Dihydroxyacetone phosphate + (4) H+ + D-Glyceraldehyde 3-phosphate | 10 | 14 | -4 | |
| RR10479 | [c]: 5-Carboxyamino-1-(5-phospho-D-ribosyl)imidazole <==> 1-(5-Phospho-D-ribosyl)-5-amino-4-imidazolecarboxylate | 14 | 11 | 3 | |
| Balanced reactions | IR01815** | [c]: Uroporphyrinogen III + (6) H+ + (2) S-Adenosyl-L-methionine --> Precorrin 2 + (2) S-Adenosyl-L-homocysteine | 88 | 88 | 0 |
| RR08939* | [c]: D-Glucose 1-phosphate <==> D-Glucose 6-phosphate | 11 | 11 | 0 |