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 : gdpofuc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 71: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 61
  Gene deletion: b2836 b3399 b4382 b3942 b1732 b1241 b0351 b4069 b2502 b4384 b2744 b3708 b1479 b2297 b2458 b3617 b3236 b1779 b2463 b3962 b1982 b1200 b0104 b2797 b3117 b1814 b4471 b3946 b2210 b0825 b4267 b0675 b2361 b2291 b3551 b1014 b2799 b2342 b3845 b2913 b4219 b1832 b1778 b2406 b0112 b2868 b0114 b0509 b3125 b0306 b1539 b3605 b2492 b0904 b1533 b1380 b1710 b2480 b1511 b4266 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.359122 (mmol/gDw/h)
  Minimum Production Rate : 0.537555 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.583009
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.567467
  EX_pi_e : 1.421521
  EX_so4_e : 0.090434
  EX_k_e : 0.070098
  EX_mg2_e : 0.003115
  EX_fe2_e : 0.002964
  EX_fe3_e : 0.002804
  EX_cl_e : 0.001869
  EX_ca2_e : 0.001869
  EX_cu2_e : 0.000255
  EX_mn2_e : 0.000248
  EX_zn2_e : 0.000122
  EX_ni2_e : 0.000116

Product: (mmol/gDw/h)
  EX_h2o_e : 51.284564
  EX_co2_e : 33.736814
  EX_h_e : 6.344593
  EX_ac_e : 1.364490
  Auxiliary production reaction : 0.537555
  EX_lac__L_e : 0.063673
  EX_ade_e : 0.000242
  DM_mththf_c : 0.000161
  DM_5drib_c : 0.000081
  DM_4crsol_c : 0.000080

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.

---

Last updated: 21-Sep-2023
Contact