MetNetComp Database [1] / Minimal gene deletions

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

Model : iML1515 [2].
Target metabolite : db4p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (9 of 13: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 19
  Gene deletion: b3916 b1241 b0351 b4069 b3114 b3952 b0903 b3115 b1849 b2296 b0767 b3617 b1851 b1779 b1200 b4015 b4388 b1723 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.410379 (mmol/gDw/h)
  Minimum Production Rate : 0.727209 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.301324
  EX_o2_e : 269.688305
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.432058
  EX_pi_e : 1.123063
  EX_so4_e : 0.103342
  EX_k_e : 0.080103
  EX_mg2_e : 0.003560
  EX_ca2_e : 0.002136
  EX_cl_e : 0.002136
  EX_cu2_e : 0.000291
  EX_mn2_e : 0.000284
  EX_zn2_e : 0.000140
  EX_ni2_e : 0.000133
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993409
  EX_h2o_e : 532.490201
  EX_co2_e : 20.929315
  EX_dha_e : 5.824680
  EX_ac_e : 0.921359
  Auxiliary production reaction : 0.727209
  DM_mththf_c : 0.000184
  DM_5drib_c : 0.000092
  DM_4crsol_c : 0.000092

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

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] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[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: 21-Sep-2023
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