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 : gdpmann_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 108: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b4069 b4384 b2744 b3708 b3008 b3752 b2297 b2458 b2407 b0583 b1982 b2797 b3117 b1814 b4471 b4374 b2361 b2291 b0261 b2406 b0452 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b3662 b0221   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.721187 (mmol/gDw/h)
  Minimum Production Rate : 0.305493 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.025518
  EX_o2_e : 274.043749
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.316225
  EX_pi_e : 1.306647
  EX_so4_e : 0.181609
  EX_k_e : 0.140771
  EX_mg2_e : 0.006256
  EX_cl_e : 0.003754
  EX_ca2_e : 0.003754
  EX_cu2_e : 0.000511
  EX_mn2_e : 0.000498
  EX_zn2_e : 0.000246
  EX_ni2_e : 0.000233
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988417
  EX_h2o_e : 547.985023
  EX_co2_e : 24.669355
  EX_ac_e : 0.419865
  Auxiliary production reaction : 0.305493
  DM_5drib_c : 0.000484
  DM_4crsol_c : 0.000161

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