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 1 - 10 of 1227
Desc Reaction GPR Genes Subsystem
Trans_tagd

D-Tagaturonate transporter

tagd[e] + h2o[c] + atp[c] -> tagd[c] + pi[c] + adp[c] ATP-driven transport
Trans_ppat

phosphonate ABC transporter ATP-binding protein

ppat[e] + atp[c] + h2o[c] -> ppat[c] + adp[c] + pi[c] (CD630_35330) or (CD630_35340) CD630_35330, CD630_35340 ATP-driven transport
Trans_gluL

amino-acid ABC transport (L-glutamate)

gluL[e] + atp[c] + h2o[c] -> gluL[c] + adp[c] + pi[c] (CD630_17750) or (CD630_17760) or (CD630_21720) or (CD630_07520) or (CD630_07510) CD630_17750, CD630_21720, CD630_07520, CD630_07510 ATP-driven transport
Trans_asnL

L-asparagine transporter

asnL[e] + atp[c] + h2o[c] -> asnL[c] + adp[c] + pi[c] (CD630_17750) or (CD630_17760) or (CD630_21720) or (CD630_07520) or (CD630_07510) CD630_17750, CD630_17760, CD630_21720, CD630_07520, CD630_07510 ATP-driven transport
Trans_glyb

glycine betaine ABC transporter

glyb[e] + atp[c] + h2o[c] -> glyb[c] + adp[c] + pi[c] (CD630_09000 and CD630_09010 and CD630_32150) CD630_09000, CD630_09010, CD630_32150 ATP-driven transport
Trans_aspL2

L-aspartate transporter

aspL[e] + atp[c] + h2o[c] -> aspL[c] + adp[c] + pi[c] (CD630_17750) or (CD630_17760) or (CD630_21720) or (CD630_07520) or (CD630_07510) CD630_17750, CD630_17760, CD630_21720, CD630_07520, CD630_07510 ATP-driven transport
Trans_ptrc

putrescine ABC transport

ptrc[e] + atp[c] + h2o[c] -> ptrc[c] + adp[c] + pi[c] (CD630_10240 and CD630_10260 and CD630_10250 and CD630_10270) CD630_10240, CD630_10260, CD630_10250, CD630_10270 ATP-driven transport
Trans_metD

D-methionine ABC transporter

metD[e] + atp[c] + h2o[c] -> metD[c] + adp[c] + pi[c] (CD630_14890 and CD630_14900 and CD630_14910 and CD630_16530) CD630_14890, CD630_14900, CD630_14910, CD630_16530 ATP-driven transport
Trans_chol

choline ABC transporter

chol[e] + atp[c] + h2o[c] -> chol[c] + adp[c] + pi[c] (CD630_09000 and CD630_09010 and CD630_32150) CD630_09000, CD630_09010, CD630_32150 ATP-driven transport
Trans_atp

sodium extrusion ABC transporter

na[e] + atp[c] + h2o[c] -> na[c] + adp[c] + pi[c] (CD630_16140) or (CD630_16590) or (CD630_05910) or (CD630_16150) CD630_16140, CD630_16590, CD630_05910, CD630_16150 ATP-driven transport