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 : mmcoa__S_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (58 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4382 b2066 b1241 b0351 b4069 b4384 b3708 b0910 b3752 b2297 b2458 b2407 b2797 b3117 b1814 b4471 b2498 b3616 b3589 b2440 b3665 b0261 b2239 b2406 b0112 b3654 b3714 b3664 b0114 b2366 b2492 b0904 b3035 b1533 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.482684 (mmol/gDw/h)
  Minimum Production Rate : 0.481818 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 20.335464
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.724049
  EX_pi_e : 1.911055
  EX_so4_e : 0.603368
  EX_k_e : 0.094217
  EX_fe2_e : 0.007752
  EX_mg2_e : 0.004187
  EX_cl_e : 0.002512
  EX_ca2_e : 0.002512
  EX_cu2_e : 0.000342
  EX_mn2_e : 0.000334
  EX_zn2_e : 0.000165
  EX_ni2_e : 0.000156
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 46.463123
  EX_co2_e : 20.752652
  EX_h_e : 10.057328
  EX_ac_e : 2.556587
  EX_ura_e : 0.569186
  Auxiliary production reaction : 0.481818
  DM_5drib_c : 0.000109
  DM_4crsol_c : 0.000108

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.

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Last updated: 21-Sep-2023
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