Metabolic Network model for C. difficile 630

Metabolic model of C.difficile: Genome-scale metabolic models consists of curated biochemical reactions and can be used to investigate genotype to phenotype relationship. These genome-wide models have the potential to predict phenotypes in various environments. icdf834 is an updated metabolic network of C. difficile that builds on iMLTC806cdf and features 1227 reactions, 834 genes, and 807 metabolites. Genes in C. difficile are linked to the reactions based on gene-protein-reaction (GPR) associations. The performance of the icdf834 model is depicted in the form of a receiver operating characteristic (ROC) curve that shows the sensitivity and specificity of the model predictions for gene essentiality. The TnSeq analysis performed under nutrient-rich condition has been used to validate the predictions using the ROC curve.

Metabolic model adapted from: Kashaf, S., Angione, C. & Lió, P. Making life difficult for Clostridium difficile: augmenting the pathogen’s metabolic model with transcriptomic and codon usage data for better therapeutic target characterization. BMC Syst Biol 11, 25 (2017). https://doi.org/10.1186/s12918-017-0395-3

TnSeq Data from: Dembek M, Barquist L, Boinett CJ, et al. High-throughput analysis of gene essentiality and sporulation in Clostridium difficile. mBio. 2015;6(2):e02383. Published 2015 Feb 24. doi:10.1128/mBio.02383-14

Explore Metabolic Reactions

Displaying 761 - 770 of 1227
Desc Reaction GPR Genes Subsystem
Sec_4abz

Secretion 4-aminobenzoate

4abz[e] -> Secretion Bookmark 
Sec_ac

Secretion acetate

ac[e] -> Secretion Bookmark 
Sec_ival

Secretion Isovalerate

ival[e] -> Secretion Bookmark 
Sec_ca2

Secretion Ca2+

ca2[e] -> Secretion Bookmark 
Sec_hxan

Secretion hypoxanthine

hxan[e] -> Secretion Bookmark 
Sec_metL

Secretion L-methionine

metL[e] -> Secretion Bookmark 
Sec_trpL

Secretion L-tryptophan

trpL[e] -> Secretion Bookmark 
Sec_actid

Secretion Acetamide

actid[e] -> Secretion Bookmark 
Sec_arab

Secretion L-arabinose

arab[e] -> Secretion Bookmark 
Sec_glcn

Secretion D-gluconate

glcn[e] -> Secretion Bookmark 
CSV