How to handle KEGG orthologous IDs involved multiple pathways

Question

[young_bioinformatician]

Hello guys,

I am a bit stuck with KEGG annotation. I have some KEGG IDs annotation of the genes with their abundance from metagenome data. Now, I want to discover them in level 3 or level 2. However, how should I consider one KEGG IDs?

Because, one KEGG ID can involve more than one pathways. So, should not it be biased?

the example for the case;

K00001: Biosynthesis of secondary metabolites, Metabolism of xenobiotics by cytochrome P450, Degradation of aromatic compounds, Microbial metabolism in diverse environments, Tyrosine metabolism, Glycolysis / Gluconeogenesis, Chloroalkane and chloroalkene degradation, Pyruvate metabolism, Naphthalene degradation, Fatty acid degradation, Retinol metabolism, Drug metabolism - cytochrome P450, Metabolic pathways K00002: Biosynthesis of secondary metabolites, Metabolic pathways

So If I have abundance for K00001 like this,

                   Sample_1 Sample_2 Sample_3    
K00001       20            50                80
K00002       10            25               40

Then;

                                                              Sample_1 Sample_2 Sample_3
*Biosynthesis of secondary metabolites   30                70             105
Metabolism of xenobiotics by cytochrome P450 20    50              80
Degradation of aromatic compounds        20               50              80
.
.
.

In that case, might some pathways be biased ?

Thanks.