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 31 - 40 of 1227Desc | Reaction | GPR | Genes | Subsystem | ||
---|---|---|---|---|---|---|
Trans_valL |
amino-acid ABC transport (L-valine) |
valL[e] + atp[c] + h2o[c] -> valL[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 | Bookmark |
Trans_proL |
amino-acid ABC transport (L-proline) |
proL[e] + atp[c] + h2o[c] -> proL[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 | Bookmark |
Trans_mg3 |
P-type magnesium transporter |
mg2[e] + atp[c] + h2o[c] -> mg2[c] + adp[c] + pi[c] | (CD630_33730) or (CD630_33770) | CD630_33730, CD630_33770 | ATP-driven transport | Bookmark |
Trans_thrL |
amino-acid ABC transport (L-threonine) |
thrL[e] + atp[c] + h2o[c] -> thrL[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 | Bookmark |
Trans_k |
potassium transport |
k[e] + atp[c] + h2o[c] -> k[c] + adp[c] + pi[c] | (CD630_15910 and CD630_15920 and CD630_15930) | CD630_15910, CD630_15920, CD630_15930 | ATP-driven transport | Bookmark |
Trans_gly |
amino-acid ABC transport (glycine) |
gly[e] + atp[c] + h2o[c] -> gly[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 | Bookmark |
Trans_mg2 |
magnesium ABC transporter |
mg2[e] + atp[c] + h2o[c] -> mg2[c] + adp[c] + pi[c] | (CD630_33750) or (CD630_16590) or (CD630_05910) | CD630_33750, CD630_16590, CD630_05910 | ATP-driven transport | Bookmark |
Trans_serL |
amino-acid ABC transport (L-serine) |
serL[e] + atp[c] + h2o[c] -> serL[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 | Bookmark |
Trans_ileL |
amino-acid ABC transport (L-isoleucine) |
ileL[e] + atp[c] + h2o[c] -> ileL[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 | Bookmark |
Trans_ribD |
ribose ABC transporter |
ribD[e] + atp[c] + h2o[c] -> ribD[c] + adp[c] + pi[c] | (CD630_03010 and CD630_03020 and CD630_03000) or (CD630_15870 and CD630_15880 and CD630_15890) | CD630_03010, CD630_03020, CD630_03000, CD630_15870, CD630_15880, CD630_15890 | ATP-driven transport | Bookmark |