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 : nadph_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4467 b4069 b4384 b3115 b1849 b2296 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b1982 b0477 b4139 b0261 b2799 b3945 b1602 b2342 b3845 b2913 b4381 b2406 b3915 b1727 b0114 b0529 b2492 b0904 b2954 b3029 b1380 b3662 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.436416 (mmol/gDw/h)
  Minimum Production Rate : 0.195860 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.995740
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.100906
  EX_pi_e : 1.008548
  EX_so4_e : 0.109898
  EX_k_e : 0.085185
  EX_fe3_e : 0.007009
  EX_mg2_e : 0.003786
  EX_ca2_e : 0.002272
  EX_cl_e : 0.002272
  EX_cu2_e : 0.000309
  EX_mn2_e : 0.000302
  EX_zn2_e : 0.000149
  EX_ni2_e : 0.000141
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 53.081427
  EX_co2_e : 37.430703
  EX_h_e : 5.267469
  EX_ac_e : 0.254075
  Auxiliary production reaction : 0.195860
  EX_gly_e : 0.016630
  EX_glyclt_e : 0.000488
  DM_5drib_c : 0.000293
  DM_4crsol_c : 0.000097

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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