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 : 2dr5p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (44 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3942 b1732 b1241 b0351 b4069 b3708 b3115 b1849 b2296 b2779 b3617 b3236 b2797 b3117 b1814 b4471 b2210 b4381 b0114 b1539 b2492 b0904 b0515 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.421916 (mmol/gDw/h)
  Minimum Production Rate : 1.263665 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 32.888331
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.556653
  EX_pi_e : 1.670648
  EX_so4_e : 0.106247
  EX_k_e : 0.082355
  EX_fe2_e : 0.006776
  EX_mg2_e : 0.003660
  EX_cl_e : 0.002196
  EX_ca2_e : 0.002196
  EX_cu2_e : 0.000299
  EX_mn2_e : 0.000292
  EX_zn2_e : 0.000144
  EX_ni2_e : 0.000136
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 46.825832
  EX_co2_e : 34.420540
  EX_h_e : 4.847974
  Auxiliary production reaction : 1.263665
  EX_ac_e : 0.971244
  DM_mththf_c : 0.000189
  DM_5drib_c : 0.000095
  DM_4crsol_c : 0.000094

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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