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 141 - 150 of 1227
Desc Reaction GPR Genes Subsystem
Trans_k3

potassium ion chanel

k[e] -> k[c] (CD630_06970) or (CD630_21420) CD630_06970, CD630_21420 Channel-type facilitator Bookmark 
Trans_zn

zinc transporter

zn2[e] -> zn2[c] (CD630_10870) or (CD630_09020) or (CD630_18310) or (CD630_21220) or (CD630_28320) or (CD630_32700) or (CD630_35200) CD630_10870, CD630_09020, CD630_18310, CD630_21220, CD630_28320, CD630_32700, CD630_35200 Channel-type facilitator Bookmark 
ID_61

isocitrate:NADP+ oxidoreductase

icit[c] + nadp[c] -> 2oglut[c] + nadph[c] + co2[c] + h[c] (CD630_08340) CD630_08340 Citrate cycle (TCA cycle) Bookmark 
ID_708

2-oxoglutarate dehydrogenase complex

2oglut[c] + coa[c] + nad[c] -> succoa[c] + co2[c] + nadh[c] + h[c] (CD630_07230 and CD630_00390) CD630_07230, CD630_00390 Citrate cycle (TCA cycle) Bookmark 
ID_370

pyruvate carboxylase

hco3[c] + pyr[c] + atp[c] + h[c] -> oxac[c] + pi[c] + adp[c] (CD630_00210) CD630_00210 Citrate cycle (TCA cycle) Bookmark 
ID_433

citrate hydro-lyase

cit[c] <=> acon[c] + h2o[c] (CD630_08330) CD630_08330 Citrate cycle (TCA cycle) Bookmark 
ID_171

isocitrate dehydrogenase (NAD+)

icit[c] + nad[c] -> 2oglut[c] + co2[c] + nadh[c] + h[c] (CD630_08340) CD630_08340 Citrate cycle (TCA cycle) Bookmark 
ID_544

acetyl-CoA:oxaloacetate C-acetyltransferase

oxac[c] + acoa[c] + h2o[c] -> cit[c] + coa[c] Citrate cycle (TCA cycle) Bookmark 
ID_310

succinyl-CoA synthase

succ[c] + coa[c] + atp[c] <=> succoa[c] + pi[c] + adp[c] (CD630_23430) CD630_23430 Citrate cycle (TCA cycle) Bookmark 
ID_606

isocitrate hydro-lyase

icit[c] <=> acon[c] + h2o[c] (CD630_08330) CD630_08330 Citrate cycle (TCA cycle) Bookmark 
CSV