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 121 - 130 of 1227
Desc Reaction GPR Genes Subsystem
ID_9718 aald[c] + acoa[c] + nadh[c] + h[c] <=> actnS[c] + nad[c] + coa[c] ( CD630_00390 and CD630_00380 and CD630_00370 and CD630_00360 ) CD630_00390, CD630_00380, CD630_00370, CD630_00360 Butanoate metabolism Bookmark 
ID_156

4-hydroxybutanoyl-CoA hydro-lyase

4hcoa[c] -> vacoa[c] + h2o[c] (CD630_23410) CD630_23410 Butanoate metabolism Bookmark 
ID_615

(R)-acetoin:NAD+ oxidoreductase

da[c] + nadh[c] + h[c] -> actnR[c] + nad[c] (CD630_11820) CD630_11820 Butanoate metabolism Bookmark 
ID_504

trans-2-enoyl-CoA reductase (NADP+)

ctnycoa[c] + nadph[c] + h[c] -> btcoa[c] + nadp[c] (CD630_03990) or (CD630_10540) CD630_03990, CD630_10540 Butanoate metabolism Bookmark 
ID_507

succinate semialdehyde hydrogenase

sucsald[c] + nadh[c] + h[c] <=> 4hbut[c] + nad[c] (CD630_23380) CD630_23380 Butanoate metabolism Bookmark 
ID_18

(R)-3-hydroxybutanoate:NAD+ oxidoreductase

r3hbat[c] + nad[c] -> aac[c] + nadh[c] + h[c] (CD630_26790) CD630_26790 Butanoate metabolism Bookmark 
ID_463

oxidoreductase acting on the CH-OH group of donors with NAD+ as acceptor

btal[c] + nadh[c] + h[c] -> buta[c] + nad[c] (CD630_03340) or (CD630_19070) or (CD630_29660) CD630_03340, CD630_19070, CD630_29660 Butanoate metabolism Bookmark 
ID_500

carbonate hydro-lyase

co2[c] + h2o[c] <=> hco3[c] + h[c] (CD630_22130) CD630_22130 Butanoate metabolism Bookmark 
ID_379

(R)-acetoin racemase

actnR[c] <=> actnS[c] Butanoate metabolism Bookmark 
ID_175

butanal:NAD+ oxidoreductase (CoA-acylating)

btcoa[c] + nadh[c] + h[c] -> btal[c] + coa[c] + nad[c] (CD630_03340) or (CD630_29660) CD630_03340, CD630_29660 Butanoate metabolism Bookmark 
CSV