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 : ins_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (27 of 38: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b2836 b4069 b4384 b2744 b3708 b2297 b2458 b2926 b0030 b2883 b1982 b2797 b3117 b1814 b4471 b4381 b2868 b4064 b4464 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.662723 (mmol/gDw/h)
  Minimum Production Rate : 0.263728 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.510378
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.301204
  EX_pi_e : 0.639267
  EX_so4_e : 0.166887
  EX_k_e : 0.129359
  EX_fe2_e : 0.010644
  EX_mg2_e : 0.005749
  EX_ca2_e : 0.003449
  EX_cl_e : 0.003449
  EX_cu2_e : 0.000470
  EX_mn2_e : 0.000458
  EX_zn2_e : 0.000226
  EX_ni2_e : 0.000214
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 49.545370
  EX_co2_e : 29.212185
  EX_h_e : 7.619043
  EX_ac_e : 0.385828
  Auxiliary production reaction : 0.263728
  EX_gsn_e : 0.017341
  EX_ade_e : 0.000446
  DM_mththf_c : 0.000297
  DM_5drib_c : 0.000149
  DM_4crsol_c : 0.000148

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
Contact