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 : dcmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (117 of 117: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 55
  Gene deletion: b4382 b3942 b1732 b1241 b0351 b4069 b4384 b3708 b1479 b3752 b2297 b2458 b3617 b2407 b3844 b3236 b1779 b2463 b3962 b1982 b1200 b0104 b2797 b3117 b1814 b4471 b3946 b2210 b0825 b4267 b3551 b1014 b2913 b4219 b1832 b1778 b2406 b0112 b0452 b2868 b0114 b0306 b1539 b3605 b2492 b0904 b1533 b1380 b0325 b1710 b2480 b0508 b4266 b3662 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.365610 (mmol/gDw/h)
  Minimum Production Rate : 1.083947 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.787766
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.201623
  EX_pi_e : 1.436616
  EX_fe3_e : 0.105274
  EX_so4_e : 0.092068
  EX_k_e : 0.071364
  EX_mg2_e : 0.003172
  EX_ca2_e : 0.001903
  EX_cl_e : 0.001903
  EX_cu2_e : 0.000259
  EX_mn2_e : 0.000253
  EX_zn2_e : 0.000125
  EX_ni2_e : 0.000118

Product: (mmol/gDw/h)
  EX_h2o_e : 51.785877
  EX_co2_e : 33.509742
  EX_h_e : 7.580759
  Auxiliary production reaction : 1.083947
  EX_ac_e : 0.863047
  EX_fe2_e : 0.099402
  EX_ade_e : 0.000246
  DM_mththf_c : 0.000164
  DM_5drib_c : 0.000082
  DM_4crsol_c : 0.000082

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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