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 : btn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (15 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b4384 b3708 b3008 b0871 b0030 b2407 b2920 b1982 b2797 b3117 b1814 b4471 b0261 b1701 b1805 b4381 b2406 b0114 b0728 b0886 b2366 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 : 0.755276 (mmol/gDw/h)
  Minimum Production Rate : 0.076381 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.788793
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.691587
  EX_pi_e : 0.728544
  EX_so4_e : 0.342956
  EX_k_e : 0.147425
  EX_fe2_e : 0.012130
  EX_mg2_e : 0.006552
  EX_cl_e : 0.003931
  EX_ca2_e : 0.003931
  EX_cu2_e : 0.000535
  EX_mn2_e : 0.000522
  EX_zn2_e : 0.000258
  EX_ni2_e : 0.000244
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.025879
  EX_co2_e : 26.629880
  EX_h_e : 7.245304
  DM_5drib_c : 0.076888
  EX_meoh_e : 0.076383
  DM_amob_c : 0.076383
  Auxiliary production reaction : 0.076381
  DM_4crsol_c : 0.000168

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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