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 (54 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4382 b4069 b4384 b3708 b3008 b3752 b3115 b1849 b2296 b2407 b2688 b2797 b3117 b1814 b4471 b3665 b0261 b2406 b2943 b3654 b3714 b3664 b0114 b2366 b2492 b0904 b0591 b2578 b1533 b3927 b2835 b0494 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.703343 (mmol/gDw/h)
  Minimum Production Rate : 0.179233 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.882223
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.850668
  EX_pi_e : 1.216146
  EX_so4_e : 0.356348
  EX_k_e : 0.137288
  EX_fe2_e : 0.011296
  EX_mg2_e : 0.006101
  EX_ca2_e : 0.003661
  EX_cl_e : 0.003661
  EX_cu2_e : 0.000499
  EX_mn2_e : 0.000486
  EX_zn2_e : 0.000240
  EX_ni2_e : 0.000227
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 47.810004
  EX_co2_e : 25.472787
  EX_h_e : 7.768231
  EX_ac_e : 0.588709
  Auxiliary production reaction : 0.179233
  DM_5drib_c : 0.000158
  DM_4crsol_c : 0.000157

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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