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 : fum_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (5 of 8: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4467 b1478 b3942 b1732 b1241 b4069 b3115 b1849 b2296 b1004 b3713 b1109 b0046 b3236 b1779 b2463 b2210 b3551 b1602 b4138 b4123 b0621 b4219 b1832 b1778 b3915 b2492 b0904 b1380 b1710 b2480 b1695 b1771 b0606 b2285 b1011 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.482440 (mmol/gDw/h)
  Minimum Production Rate : 0.503085 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.272357
  EX_o2_e : 287.095569
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.210315
  EX_pi_e : 0.465365
  EX_so4_e : 0.121488
  EX_k_e : 0.094169
  EX_mg2_e : 0.004185
  EX_ca2_e : 0.002511
  EX_cl_e : 0.002511
  EX_cu2_e : 0.000342
  EX_mn2_e : 0.000333
  EX_zn2_e : 0.000165
  EX_ni2_e : 0.000156
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992252
  EX_h2o_e : 551.366171
  EX_co2_e : 37.623958
  EX_fum_e : 0.503085
  EX_ac_e : 0.280870
  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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