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The multi-level design provides the mechanism for matching reaction and mass transfer rates, and for optimizing the volumetric productivity.
Specifically, peripheral antennae complexes (in this case IsiA supercomplexes) are produced at levels closely matching reaction center abundance when iron is limiting and nitrate is low.
we identified matching columns (reactions), assuming that identical stoichiometric relationships between a set of metabolites represented a matching reaction between BioCyc and KEGG.
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We call such a pair of matching reactions a building block (BB).
Although not taken into account when matching reactions, the direction of a reaction and the compartment(s) as indicated by the source database are shown in a C2Card.
We did not consider e-, H2O H2O in matching reactions as with respect to these particular metabolites reactions are not always balanced.
For integration purposes, we also provide an automatically derived overview of all reactions in which matching reactions are aligned, along with their associated genes, EC number and pathways (Additional file 13).
Martin Johnson was, unsurprisingly, far less forthcoming in his post- match reaction.
The SMARTS language is supported well including features such as stereochemistry, component grouping, and atom maps (to match reaction transformations).
ΔCq represents the difference between the Cq value for the mismatched reaction minus the Cq value for the matched reaction.
As evident in Table 8, SubMAP matches reaction R00565 (catalyzed by enzyme 2.1.4.1) with reaction R00554 (catalyzed by enzyme 2.7.3.3), although the two reactions belong to different parts of the pathways.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com