To circumvent some of the reaction gaps, proteins identified in a M. suis proteomic study described elsewhere were used [48].
For this PGDB, the reaction gap-filler did not help, as EcoCyc was already well curated in the sense of containing the required reactions, such that no truly missing reactions are needed to be imported from MetaCyc.
Our reaction gap-filler has limited flexibility regarding compartmentation; reactions can be gap-filled into the same compartment as the reaction occupied in MetaCyc, but cannot be shifted arbitrarily among compartments this issue will be remedied in a subsequent release.
A common step in such reconstruction refinements is filling reaction gaps to decrease the numbers of dead-end metabolites and enhance the network connectivity.
These results suggest the usefulness of the proposed method not only for filling in the reaction gaps among existing pathways but also for de novo reconstruction of a series of reactions.
Reference functional databases such as KEGG [ 49] and AraCyc [ 50] are frequently used as the backbone for metabolic reconstruction, which needs to be further complemented by algorithms that build the genome-wide metabolic network, fill in reaction gaps and validate predictions [ 51].
Two other Cdc42 regulators are represented implicitly by first-order reactions: GAPs promote GTP hydrolysis by Cdc42 (rate constant k2b), and the GDI reversibly exchanges GDP-Cdc42 between membrane and cytoplasm (rate constants k5a and k5b).
The fit of the data from Figure 5A to a single-exponential decay gave a kobs of 2.7 × 10 4 s–1 for the disappearance of GAP. Figure 5B shows the change with time in the fractional product yields (fP obs (eq 4) for DHAP, d-DHAP, and d-GAP during a 150 min L6RM-catalyzed reaction of GAP.
DOI: http://dx.doi.org/10.7554/eLife.02536.013 10.7554/eLiFigure36 figuregure 6—figure supplement 1. Aldolase C enzymatic reaction products GAP and DHAP increase the activity in lobules III and X.
Inhibition of the L6RM-catalyzed reaction of GAP in the presence of 2-phosphoglycolate (PGA, 1 10 mM) was examined at pH 7.5 (I = 0.1, NaCl) by determining values of kcat/ Km from the slopes of linear correlations of four or five values of vi/[E] against [GAP] for reactions at several different PGA concentrations.
Based on the sequence scaffolds, synteny to the S. cerevisae genome, and by using directed polymerase chain reaction for gap closure, we generated a chromosomal map of S. carlsbergensis consisting of 29 unique chromosomes.
