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The classification of reactions into pathways was retrieved from the KEGG database.
The following step aimed to investigate in detail the classification of reactions into the actual pathways.
To address this question, I took advantage of the biochemical pathway classification of reactions in KEGG [ 36].
The classification of reactions into pathways is somewhat subjective, since it can be implemented in a varied manner.
Moreover, the classification of reactions into phylogenetic reaction sets is generally in agreement with classifications obtained using different procedures [ 15].
Classification of reactions by functional category as presented in supplementary figure S1 (Supplementary Material online) follows previous authors (Reed et al. 2003; Duarte et al. 2004).
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In examining chemical reactions, it is useful to consider several general subjects: (1) factors that influence the course of chemical reactions, (2) energy changes involved in the course of a typical reaction, (3) factors that reveal the mechanism of a reaction, and (4) the classification of reaction mechanisms.
As in some earlier work, the principal results rely on a classification of reaction networks by means of an easily computed non-negative integer index called the deficiency.
For these reasons, although these approaches produced very interesting results for specific tasks, they are not easily applicable to the task of generating general global classifications of reactions.
The classification of these reactions as gas liquid, gas liquid solid, gas liquid liquid and gas liquid liquid solid reactions and related reaction engineering issues are also summarized.
EzCatDB also provides a hierarchic classification of enzyme reactions, RLCP, which clusters the same reaction types together based on basic Reaction (R), Ligand group involved in catalysis (L), type of Catalytic mechanism (C), and residue/cofactors located on Proteins (P) (Nagano, 2005).
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