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 : coa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (78 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 52
  Gene deletion: b4467 b1478 b0474 b2518 b1241 b3831 b4069 b3708 b3752 b2297 b2458 b2926 b2781 b3844 b1004 b3713 b1109 b0046 b3236 b1759 b0937 b2797 b3117 b1814 b4471 b4161 b0411 b1701 b1805 b2799 b3945 b1602 b2913 b4381 b2406 b3654 b3714 b3664 b4064 b4464 b1539 b2492 b0904 b1533 b1380 b3918 b4042 b1511 b4141 b1798 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.454444 (mmol/gDw/h)
  Minimum Production Rate : 0.100487 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.942227
  EX_o2_e : 286.847072
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.611364
  EX_pi_e : 0.739819
  EX_so4_e : 0.214925
  EX_k_e : 0.088704
  EX_mg2_e : 0.003942
  EX_ca2_e : 0.002365
  EX_cl_e : 0.002365
  EX_cu2_e : 0.000322
  EX_mn2_e : 0.000314
  EX_zn2_e : 0.000155
  EX_ni2_e : 0.000147
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992701
  EX_h2o_e : 551.812585
  EX_co2_e : 37.906377
  EX_ac_e : 0.365058
  EX_3hpp_e : 0.182742
  Auxiliary production reaction : 0.100487
  EX_glyclt_e : 0.025600
  DM_mththf_c : 0.000204
  DM_5drib_c : 0.000102
  DM_4crsol_c : 0.000101

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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