TABLE 2.

Discrepancies between experimental identification and model prediction for essential and nonessential genesa

RationaleSubsystemGene(s) (Blattner no.)
False negatives
    Molecules not included in biomassUbiquinone biosynthesisubiG (b2232); ubiH (b2907)
Pyridoxine biosynthesispdxA (b0052); pdxB (b2320); pdxH (b1638); pdxJ (b2564)
Thiamine biosynthesisiscC (b2530)
    Model includes alternative pathways/     isozymesAmino acid biosynthesiscarA (b0032); carB (b0033); glpD (b3426); glyA (b2551); proA (b0243); proB (b0242); thrB (b0003); thrC (b0004)
    Model predicts impaired but not lethal     phenotypeATP synthaseatpA (b3734); atpB (b3738); atpC (b3731); atpF (b3736); atpG (b3733); atpH (b3735)
    Regulatory effect on glpKPTS/PEP metabolismcrr (b2417); glpK (b3926); ppc (b3956); ptsI (b2416); fruR (b0080)
False positives
    Model biomass components which     might not be essential componentsFatty acid and lipid biosynthesiscls (b1249); fabF (b1095)
GlycogenglgA (b3429); glgC (b3430)
LPS synthesisdgkA (b4042); gmhA (b0222); gmhB (b0200); lpxL (b1054); msbB (b1855); rfaC (b3621); rfaD (b3619); rfaE (b3052); rfaF (b3620); rfaG (b3631); rfaI (b3627); rfaJ (b3626); rfaL (b3622)
Spermidine synthesispfs (b0159); speD (b0120); speE (b0121)
    Unaccounted-for transport mechanismsAmmonium transportamtB (b0451)
Glycerol transportglpF (b3927)
Sulfate transportcysW (b2423)
    Unaccounted-for metabolic enzymesArginine biosynthesisargB (b3959); argC (b3958); argD (b3359); argG (b3172)
Aspartate biosynthesisaspC (b0928)
Branced amino acid biosynthesisilvY (b3773); ilvE (b3770); lrp (b0889)
Central metabolicaldA (b1415)
Cofactor biosynthesiscoaA (b3974); coaE (b0103); pabC (b1096)
Glycolyticpgi (b4025)
Lysine biosynthesisdapF (b3809); ushA (b0480); lysR (b2839)
Nucleotide biosynthesis and salvagepyrI (b4244); trxB (b0888); ndk (b2518)
  • a Twenty-six false-negative cases in which the model incorrectly predicted growth of the gene deletion strain were identified, in addition to 42 false-positive cases in which the model incorrectly predicted that genes were essential. Each case is grouped based on the likely rationale for the discrepancy and the gene functional annotation.