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 : adpglc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (52 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4069 b4384 b2744 b3708 b3008 b3752 b3115 b1849 b2296 b2883 b1779 b1982 b2797 b3117 b1814 b4471 b4374 b2361 b2291 b0261 b0411 b1701 b1805 b4381 b2868 b4064 b4464 b0114 b1539 b2492 b0904 b2578 b1533 b3927 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.648913 (mmol/gDw/h)
  Minimum Production Rate : 0.274878 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.510496
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.386220
  EX_pi_e : 1.175700
  EX_so4_e : 0.163409
  EX_k_e : 0.126663
  EX_fe2_e : 0.010422
  EX_mg2_e : 0.005629
  EX_ca2_e : 0.003378
  EX_cl_e : 0.003378
  EX_cu2_e : 0.000460
  EX_mn2_e : 0.000448
  EX_zn2_e : 0.000221
  EX_ni2_e : 0.000210
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 49.197959
  EX_co2_e : 28.206424
  EX_h_e : 7.168519
  EX_ac_e : 0.377788
  Auxiliary production reaction : 0.274878
  EX_ade_e : 0.000726
  DM_5drib_c : 0.000435
  DM_4crsol_c : 0.000145

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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