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 : 2omph_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (40 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b1241 b0351 b4069 b2502 b4384 b2744 b3115 b1849 b2296 b3617 b2407 b3665 b0675 b2361 b4381 b0112 b3654 b3714 b3664 b0114 b0529 b2492 b0904 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.533459 (mmol/gDw/h)
  Minimum Production Rate : 0.225302 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 18.481904
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.248771
  EX_pi_e : 0.514577
  EX_so4_e : 0.134336
  EX_k_e : 0.104127
  EX_fe2_e : 0.008568
  EX_mg2_e : 0.004628
  EX_ca2_e : 0.002777
  EX_cl_e : 0.002777
  EX_cu2_e : 0.000378
  EX_mn2_e : 0.000369
  EX_zn2_e : 0.000182
  EX_ni2_e : 0.000172
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 41.356476
  EX_co2_e : 23.328591
  EX_h_e : 5.699666
  EX_ac_e : 0.310572
  EX_thymd_e : 0.243732
  DM_mththf_c : 0.225541
  Auxiliary production reaction : 0.225302
  DM_5drib_c : 0.000120
  DM_4crsol_c : 0.000119

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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