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Inter-individual variation was also evident in the completion ratio of the module for vitamins.
The completion ratio of each KEGG module was compared between humans and human gut microbiomes to illustrate their metabolic linkage.
We have developed a new evaluation method for the potential functionome, based on the completion ratio of Kyoto Encyclopedia of Genes and Genomes (KEGG) functional modules.
Similarly, the completion ratio of the KEGG modules (M00135_1 and M00136_1) for γ-aminobutyric acid (GABA) varied among individuals, and Gammaproteobacteria mainly contributed to GABA production.
The completion ratio of all KEGG functional modules in each organism was calculated based on a Boolean algebra-like equation (Additional file 1: Table S6).
In this study, we first calculated the completion ratio of each KEGG module in reference species whose genomic sequences have been completely determined.
Similar(48)
Thus, we first examined distribution patterns of the completion ratios of the KEGG modules in the 768 prokaryotic species whose genomic sequences have been completed (Additional file 1: Table S1).
However, since most of the species, except for 58 species within Gammaproteobacteria, do not have the genes assigned to K11258 of the acetolactate synthase II small subunit, the module completion ratio in the remaining 518 species becomes 85.7%.
Thus, when the module completion ratio is low, the relationship between the module completion ratio of the targeted module and others to which the same KO identifiers are assigned should be considered.
Diversified: the modules that varies in the module completion ratio among 768 prokaryotic species, Non-prokaryotic: the modules not to be completed by any prokaryotic species.
The module completion ratio (see the section below) was calculated for each submodule in this study to examine fine-grained functional categories.
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