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 : imacp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (91 of 103: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b3399 b4382 b4069 b4384 b2744 b3708 b3008 b2297 b2458 b0160 b2797 b3117 b1814 b4471 b2440 b0675 b2361 b2291 b0261 b0411 b3709 b2406 b3161 b0112 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b0886 b2366 b2492 b0904 b3035 b2578 b1533 b3927 b1473 b0494 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.705791 (mmol/gDw/h)
  Minimum Production Rate : 0.899283 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.756477
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.421052
  EX_pi_e : 1.580094
  EX_so4_e : 0.177732
  EX_k_e : 0.137766
  EX_fe2_e : 0.011336
  EX_mg2_e : 0.006123
  EX_ca2_e : 0.003674
  EX_cl_e : 0.003674
  EX_cu2_e : 0.000500
  EX_mn2_e : 0.000488
  EX_zn2_e : 0.000241
  EX_ni2_e : 0.000228
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 48.846703
  EX_co2_e : 24.813008
  EX_h_e : 8.694560
  Auxiliary production reaction : 0.899283
  EX_ac_e : 0.410902
  DM_5drib_c : 0.000159
  DM_4crsol_c : 0.000157

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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