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 : pnto__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (52 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3399 b3942 b1732 b1241 b0351 b4069 b2502 b2744 b3708 b0871 b2297 b2458 b2779 b2925 b2097 b3236 b2883 b2797 b3117 b1814 b4471 b3616 b3589 b3946 b2210 b0825 b4374 b2361 b2291 b0114 b1539 b2492 b0904 b1533 b1518 b1813 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.321263 (mmol/gDw/h)
  Minimum Production Rate : 0.961771 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.099110
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.431597
  EX_pi_e : 0.309892
  EX_so4_e : 0.080900
  EX_k_e : 0.062708
  EX_fe2_e : 0.005160
  EX_mg2_e : 0.002787
  EX_ca2_e : 0.001672
  EX_cl_e : 0.001672
  EX_cu2_e : 0.000228
  EX_mn2_e : 0.000222
  EX_zn2_e : 0.000110
  EX_ni2_e : 0.000104

Product: (mmol/gDw/h)
  EX_h2o_e : 42.339844
  EX_co2_e : 29.559958
  EX_h_e : 7.987982
  EX_pyr_e : 2.372252
  Auxiliary production reaction : 0.961771
  EX_ac_e : 0.739759
  DM_oxam_c : 0.000216
  DM_mththf_c : 0.000144
  EX_glyc__R_e : 0.000107
  DM_5drib_c : 0.000072
  DM_4crsol_c : 0.000072

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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