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Table 3 List of 76 predicted C. difficile essential gene and essentiality of their B. subtilis homologs

From: A curated C. difficile strain 630 metabolic network: prediction of essential targets and inhibitors

Essentiality ofB. subtilishomolog

PredictedC. difficileessential genesa

Essential (46)

accA3, accB3, accC3, accD3, acpS2?, adk2?, asd 3, cdsA3, cmk2, coaE3?, dapF 3, dapH 3, ddl 3, dxr 3, dxs 3, fabD 3?, fabF 3?, glmU3, gmk3, guaB2, ispD 3, ispE 3, ispF 3, ispG 3, ispH 3, metK2, mnaA3, murA 3?, murB 3, murC 3, murD 3, murE 3?, murF 3, murG 3, nadD3, nadE 3, pgsA 3?, plsX3, prs3, CD0119 3, CD0244 3*, CD10493, CD24393, CD35432, CD35503*, pgk1 (15.48%)

Non-essential (22)

coaBC3, coaD3, crt13?, fabH 3, fabZ3, guaA3, ispA3, metF1*, pdp3*, ribC3?, CD05572?, CD19663*, CD2256 2*, CD25412*, CD2549 2*?, CD35553, CD35961, pykF1 (15.51%), CD09941*? (15.08%), serA1? (15.08%), ackA 1 (14.74%), asnA1? (5.76%)

No B. subtilis homolog (8)

cat1 1*, ntpA1* (10.31%), ntpB1 (10.31%), ntpC1 (10.31%), ntpD1* (10.31%), ntpE1* (10.31%), ntpF1* (10.31%), ntpK1* (10.31%)

  1. Number in parenthesis represent the loss of biomass according to FBA. Those without number prevent the production of biomass or were identified only by SA. Genes in bold (25 in total) do not have a human functional homolog. The 4 genes in italics have a human homolog shown to be essential when their associated reactions are removed from RECON2.
  2. 1Genes predicted as essential exclusively by FBA analysis (16 in total).
  3. 2Genes predicted as essentials by the SA analysis (10 in total).
  4. 3Genes predicted as essentials by both FBA and SA (50 in total).
  5. ?Genes shown to be down-regulated in vivo (9 in total) [57].
  6. ?Genes shown to be up-regulated in vivo (6 in total) [57].
  7. *Genes not present in the Database of Essential Genes (DEG) (15 in total) [56].
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BMC Systems Biology

ISSN: 1752-0509

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