MetNetComp Database / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iHN637 [2].
Target metabolite : pep_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (8 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 16
  Gene deletion: CLJU_RS05830 CLJU_RS08100 CLJU_RS08095 CLJU_RS04120 CLJU_RS09865 CLJU_RS09915 CLJU_RS20875 CLJU_RS02035 CLJU_RS01155 CLJU_RS07210 CLJU_RS03475 CLJU_RS08715 CLJU_RS15865 CLJU_RS18495 CLJU_RS06260 CLJU_RS01595   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.054685 (mmol/gDw/h)
  Minimum Production Rate : 0.648372 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fru_e : 5.000000
  EX_nh4_e : 1.266006
  EX_pi_e : 0.711732
  EX_k_e : 0.010455
  EX_so4_e : 0.010326
  EX_fe2_e : 0.000756
  EX_mg2_e : 0.000465
  EX_ca2_e : 0.000279
  EX_cl_e : 0.000279
  EX_fol_e : 0.000049
  EX_cu2_e : 0.000038
  EX_mn2_e : 0.000037
  EX_ribflv_e : 0.000024
  EX_zn2_e : 0.000018
  EX_ni2_e : 0.000017
  EX_cobalt2_e : 0.000014
  EX_thm_e : 0.000012

Product: (mmol/gDw/h)
  EX_co2_e : 8.029134
  EX_etoh_e : 7.526983
  EX_h2o_e : 3.696997
  EX_h_e : 1.395328
  Auxiliary production reaction : 0.648372
  EX_lys__L_e : 0.424748
  EX_ac_e : 0.018225
  DM_succ_c : 0.006915
  EX_ala__D_e : 0.001554
  EX_glyc_e : 0.001257
  DM_mththf_c : 0.000122

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Orth, J. D., Fleming, R. M., Palsson, B. Ø. (2010). Reconstruction and use of microbial metabolic networks: the core Escherichia coli metabolic model as an educational guide. EcoSal plus, 4(1).
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

Last updated: 27-Sep-2023
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