Table 1.
Typical problems arising from automatic metabolic networks reconstruction and examples of dealing with them
|
Problem |
Example |
|---|---|
| 1) Substrate specificity is insufficiently or wrongly defined. | The ORF SCO4384 encodes an enoyl-CoA hydratase with assigned E.C. number 4.2.1.17, and the enzyme acts on a wide range of 3-hydroxyacyl-CoA compounds. Judging from the neighbor ORF SCO4383, which encodes a 4-coumarate: coenzyme A ligase and is positioned in the same regulon, SCO4384 more likely catalyzes hydration of activated 4-coumarate and hence is involved in the secondary metabolism. |
| 2) Reversibility is not defined. | Pyruvate carboxylase (E.C. 6.4.1.1) is shown in KEGG as acting in both directions even though it is known to be irreversible because of thermodynamic constraints prevailing in most cells, that is, the carboxylation of pyruvate to oxaloacetate is associated with the cleavage of a high-energy phosphate bond in ATP resulting in the formation of AMP and pyrophosphate, whereas the decarboxylation of oxaloacetate to pyruvate does not result in the formation of ATP. |
| 3) Enzyme subunits are shown as catalyzing a reaction independently although they are active only in a complex. | The ORFs SCO0216-0219 form a four-subunit complex with a nitrate reductase activity, while in KEGG each of these ORFs is assigned the given function, basically indicating that each of these four ORFs encodes an isoenzyme. |
| 4) Cofactor requirements are often specific for the given organism and have to be found elsewhere. | Valine dehydrogenase E.C. 1.4.1.8 is given as NADP+-dependent in KEGG; however, it was experimentally determined to use NAD+ as the preferred hydrogen acceptor (Navarrete et al. 1990). |
| 5) Several reactions that are necessary for making a functional cell have not been assigned a corresponding ORF.
|
Histidinol phosphatase E.C. 3.1.3.15 is an enzyme in the linear histidine biosynthesis pathway. It was included in the model
even though the gene was not found in the genome of S. coelicolor A3(2).
|
