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 : mnl1p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (50 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b3553 b1478 b1241 b4069 b3708 b2297 b2458 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b0207 b3012 b2797 b3117 b1814 b4471 b1033 b0261 b2799 b1602 b2913 b4381 b3915 b2366 b2492 b0904 b1781 b3001 b1380 b0325 b1771 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.476194 (mmol/gDw/h)
  Minimum Production Rate : 0.317157 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.530673
  EX_o2_e : 286.314715
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.951839
  EX_pi_e : 0.776496
  EX_so4_e : 0.119915
  EX_k_e : 0.092950
  EX_mg2_e : 0.004131
  EX_ca2_e : 0.002479
  EX_cl_e : 0.002479
  EX_cu2_e : 0.000338
  EX_mn2_e : 0.000329
  EX_zn2_e : 0.000162
  EX_ni2_e : 0.000154
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992352
  EX_h2o_e : 551.377151
  EX_co2_e : 36.985794
  Auxiliary production reaction : 0.317157
  EX_ac_e : 0.277233
  EX_hxan_e : 0.202247
  DM_5drib_c : 0.000107
  DM_4crsol_c : 0.000106

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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