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 : amet_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (58 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3399 b2502 b2744 b3708 b3008 b0871 b1982 b2797 b3117 b1814 b4471 b2440 b0675 b2361 b2291 b4381 b2868 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b2240 b4141 b1798 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.583559 (mmol/gDw/h)
  Minimum Production Rate : 0.067147 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.792745
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.706846
  EX_pi_e : 0.562905
  EX_so4_e : 0.214099
  EX_k_e : 0.113907
  EX_fe2_e : 0.009373
  EX_mg2_e : 0.005062
  EX_ca2_e : 0.003037
  EX_cl_e : 0.003037
  EX_cu2_e : 0.000414
  EX_mn2_e : 0.000403
  EX_zn2_e : 0.000199
  EX_ni2_e : 0.000188
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 51.390876
  EX_co2_e : 35.037091
  EX_h_e : 5.564989
  Auxiliary production reaction : 0.067147
  EX_hxan_e : 0.000393
  DM_mththf_c : 0.000261
  DM_5drib_c : 0.000131
  DM_4crsol_c : 0.000130

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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