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 : alaala_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (13 of 17: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 16
  Gene deletion: CLJU_RS05830 CLJU_RS08100 CLJU_RS08095 CLJU_RS06265 CLJU_RS18515 CLJU_RS20875 CLJU_RS02035 CLJU_RS01155 CLJU_RS19980 CLJU_RS15035 CLJU_RS12480 CLJU_RS07210 CLJU_RS03475 CLJU_RS08715 CLJU_RS15865 CLJU_RS18530   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.117412 (mmol/gDw/h)
  Minimum Production Rate : 1.113679 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fru_e : 5.000000
  EX_nh4_e : 3.196565
  EX_pi_e : 0.136039
  EX_k_e : 0.022447
  EX_so4_e : 0.022171
  EX_fe2_e : 0.001623
  EX_mg2_e : 0.000998
  EX_ca2_e : 0.000599
  EX_cl_e : 0.000599
  EX_fol_e : 0.000105
  EX_cu2_e : 0.000081
  EX_mn2_e : 0.000079
  EX_ribflv_e : 0.000052
  EX_zn2_e : 0.000039
  EX_ni2_e : 0.000037
  EX_cobalt2_e : 0.000029
  EX_thm_e : 0.000026

Product: (mmol/gDw/h)
  EX_co2_e : 6.591073
  EX_h2o_e : 6.568443
  EX_etoh_e : 5.692722
  EX_h_e : 2.917497
  Auxiliary production reaction : 1.113679
  EX_lys__L_e : 0.037469
  DM_succ_c : 0.014847
  EX_ala__D_e : 0.003336
  DM_mththf_c : 0.000262

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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