EnzymeDistribution: Distribution Of Simple Sugar Degradation Enzymes In Microbes

In MolyWang/microCompet: Identify A Microbe's Potential Nutrition Competitor From Microbiota

Distribution Of Simple Sugar Degradation Enzymes In Microbes

Description

The distribution of 66 sugar degradation enzymes in 9 representative human microbiota members. Because some enzymes can catalyze more than one reactions, this dataset has more than 66 rows. When reading this dataset, "0" suggests the enzyme represented by the row is not present in the column microbe, while "1" suggests it's present

Usage

EnzymeDistribution

Format

A matrix with 71 rows (genes) and 13 variables

Gene

Name of gene encoding this sugar degradation enzyme.

Reaction.EC

EC category of this enzyme, indicating its reaction type.

Enzyme

Full name of the enzyme

Sugar

The sugar degradation pathway this enzyme invoved in.

Lplan

Lactobacillus plantarum

Ecoli

Escherichia coli

Blong

Bifidobacterium longum

Paeru

Pseudomonas aeruginosa

Bthet

Bacteroides thetaiotaomicron

Cbotu

Clostridium botulinum

Enter

Enterobacter sp. EA-01

Kvari

Klebsiella variicola

Spneu

Streptococcus pneumoniae

Details

E. coli is usually treated as a positive control species because it survives in minimal media and can synthesize and degrade almost all common sugars.

Source

Genomes downloaded from NCBI, see dataset GenomesInfo for details.

Examples

 ## Not run: 
   head(EnzymeDistribution)
 
## End(Not run)

MolyWang/microCompet documentation built on Feb. 26, 2023, 9:29 p.m.