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Based on the gene-protein-reaction (GPR) model of E.coli_iAF1260 and the method of constraint-based analysis, we first calculated the metabolic flux distribution of E.coli_iAF1260 and defined three types of key genes (genes related to many reactions, genes related to high flux reactions, genes related to the hubs of correlated reaction sets) which related to its metabolism. Then we analyzed the impact of key gene deletion on the metabolic flux redistribution of E.coli_iAF1260 and on its high-flux backbone (HFB). We find that the deletion of these key genes will greatly affect the metabolic flux distribution but will affect flux backbone trivially. Because the in silico model of E.coli_iAF1260 is tested by many experiments, thus is credible, we can conclude that the result we get has biological significances.