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 : cpmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (22 of 38: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b1241 b0351 b4069 b4384 b2744 b3115 b1849 b2296 b0030 b2883 b0907 b1982 b3616 b3589 b1623 b0411 b4381 b2868 b0114 b0529 b2492 b0904 b3662 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.555875 (mmol/gDw/h)
  Minimum Production Rate : 1.051147 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.101352
  EX_nh4_e : 11.319185
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.587347
  EX_so4_e : 0.139980
  EX_k_e : 0.108503
  EX_fe2_e : 0.008928
  EX_mg2_e : 0.004822
  EX_ca2_e : 0.002893
  EX_cl_e : 0.002893
  EX_cu2_e : 0.000394
  EX_mn2_e : 0.000384
  EX_zn2_e : 0.000190
  EX_ni2_e : 0.000180
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 48.524387
  EX_co2_e : 21.096862
  EX_h_e : 12.122098
  EX_ac_e : 2.749861
  Auxiliary production reaction : 1.051147
  EX_hxan_e : 0.014545
  EX_ade_e : 0.000374
  DM_mththf_c : 0.000249
  DM_5drib_c : 0.000125
  DM_4crsol_c : 0.000124

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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