Biology Reference
In-Depth Information
grow
in silico
on glucose in minimal medium. The remaining gaps identifi ed in the
model completion step (Figure 1) were mostly single missing steps in the pathway
for which there is experimental evidence of operation (e.g., a compound is consumed
but not produced, and no alternative pathways exist). It should be noted that for some
gaps, there is more than one combination of reactions with which the gap could be
closed [34]. In cases where more than one gap closure method was available, the deci-
sion of which to use was made based on similarity queries to related bacteria.
The iJP815 model includes 289 reactions for which non-zero fl ux values cannot
be obtained under any environmental condition while enforcing the pseudo steady-
state assumption (PSSA). We term these reactions “unconditionally blocked” meaning
that they are unable to function because not all connections could be made with the
information available. Three hundred sixty-two metabolites that are only involved in
these reactions are classifi ed as “unbalanced metabolites”. Another important subset of
model reactions is the “weakly annotated” set, which means that all the genes assigned
to these 57 reactions are currently annotated as coding for “putative” or “family” pro-
teins. The relationships between all the subsets are shown in Table 1 and Figures 2 and 3.
Figure 2.
Schematic representation of various reaction classes and their interdependency.
The areas
of the squares correspond to the sizes of the subsets.
Figure 3.
Assignment of the reactions to the particular pathways.
