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 : gua_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (104 of 123: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b2836 b3399 b3942 b1732 b2744 b3708 b3008 b0871 b2926 b3844 b3236 b2883 b2797 b3117 b1814 b4471 b2210 b4381 b4064 b4464 b0114 b1539 b2492 b0904 b1533 b0515 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.700741 (mmol/gDw/h)
  Minimum Production Rate : 0.158942 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.420201
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.373598
  EX_pi_e : 0.675939
  EX_so4_e : 0.176461
  EX_k_e : 0.136780
  EX_fe2_e : 0.011255
  EX_mg2_e : 0.006079
  EX_ca2_e : 0.003647
  EX_cl_e : 0.003647
  EX_cu2_e : 0.000497
  EX_mn2_e : 0.000484
  EX_zn2_e : 0.000239
  EX_ni2_e : 0.000226
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 50.543773
  EX_co2_e : 30.430566
  EX_h_e : 7.244342
  Auxiliary production reaction : 0.158942
  EX_alltn_e : 0.002736
  EX_mththf_e : 0.000314
  DM_5drib_c : 0.000158
  DM_4crsol_c : 0.000156

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