Skip to main content

Table 1 Variables that were used to compare the panEFMs and pan-reactomes of 46 prokaryote families (Fig. 4, Table S6)

From: Nutrition or nature: using elementary flux modes to disentangle the complex forces shaping prokaryote pan-genomes

Variable

Description

NicheBreadth

Predicted niche breadth from global environmental sequencing datasets (see Methods)

diversity(panEFMs)

The diversity between reaction frequency of panEFMs sampled in different virtual environments (Average squared pairwise Euclidean distance)

fluidity(panEFMs)

The average dissimilarity between panEFMs independently of the random environments in which it was sampled

pan(panEFMs)

Total reactions that are included in at least one of the panEFMs sampled in different virtual environments

pan(Reactomes)

The number of reactions found in the pan-reactome of a prokaryote family

size(panEFMs)

The average size of panEFMs sampled in different virtual environments

size(Reactomes)

The average size of the natural reactomes from a prokaryote family

core(panEFMs)

The number of reactions that are present in at least 98% of the panEFMs sampled in different virtual environments

core(Reactomes)

The number of reactions present in at least 98% of the natural reactomes from a prokaryote family

shell(panEFMs)

The number of reactions that are present in 3 to 98% of all the panEFMs sampled in different virtual environments

shell(Reactomes)

The number of reactions that are present in 3 to 98% of the natural reactomes from a prokaryote family

cloud(panEFMs)

The number of reactions present in up to 3% of the panEFMs sampled in different virtual environments

cloud(Reactomes)

The number of reactions present in up to 3% of the natural reactomes from a prokaryote family

diversity(Metabs)

The diversity between metabolite usage profiles of panEFMs sampled in different virtual environments (Average squared pairwise Euclidean distance)

EnvDReacs

The number of reactions with an environment-driven score (EDS) EDS significantly > 0 (adj. p < 0.05 on a Z-test)

EnvDMetabs

The number of metabolites that are significantly associated with reactions with a non-zero EDS