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 : aps_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3553 b4382 b3831 b4069 b4384 b3752 b3926 b3115 b1849 b2296 b2407 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b1033 b0261 b0411 b3945 b1602 b2913 b3915 b0114 b0529 b2492 b0904 b1380 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.474380 (mmol/gDw/h)
  Minimum Production Rate : 0.218923 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.263853
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.219999
  EX_pi_e : 0.676512
  EX_so4_e : 0.338381
  EX_k_e : 0.092596
  EX_fe3_e : 0.007619
  EX_mg2_e : 0.004115
  EX_cl_e : 0.002469
  EX_ca2_e : 0.002469
  EX_cu2_e : 0.000336
  EX_mn2_e : 0.000328
  EX_zn2_e : 0.000162
  EX_ni2_e : 0.000153
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 53.095871
  EX_co2_e : 37.737284
  EX_h_e : 5.301479
  EX_ac_e : 0.276177
  Auxiliary production reaction : 0.218923
  EX_glyc_e : 0.015436
  EX_hxan_e : 0.000531
  DM_5drib_c : 0.000318
  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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