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 : prpncoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (42 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3399 b1241 b0351 b4069 b2502 b4384 b2744 b3708 b2297 b2458 b2797 b3117 b1814 b4471 b3616 b3589 b3665 b4374 b0675 b2361 b2291 b1701 b1805 b0112 b3654 b3714 b3664 b0114 b2366 b2492 b0904 b1533 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.506643 (mmol/gDw/h)
  Minimum Production Rate : 0.505809 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 20.109664
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.012364
  EX_pi_e : 2.006139
  EX_so4_e : 0.633392
  EX_k_e : 0.098893
  EX_fe2_e : 0.008137
  EX_mg2_e : 0.004395
  EX_ca2_e : 0.002637
  EX_cl_e : 0.002637
  EX_cu2_e : 0.000359
  EX_mn2_e : 0.000350
  EX_zn2_e : 0.000173
  EX_ni2_e : 0.000164
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 45.697690
  EX_co2_e : 21.696660
  EX_h_e : 8.856376
  EX_ac_e : 2.683713
  Auxiliary production reaction : 0.505809
  EX_mththf_e : 0.000227
  DM_5drib_c : 0.000114
  DM_4crsol_c : 0.000113

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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