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 : hisp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (53 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4467 b1478 b3399 b1241 b4069 b4384 b2744 b3115 b1849 b2296 b0030 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b1623 b0261 b0411 b2799 b3945 b1602 b0153 b2913 b4381 b0529 b2492 b0904 b3035 b1380 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.384909 (mmol/gDw/h)
  Minimum Production Rate : 1.190605 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.728943
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.771244
  EX_pi_e : 1.561891
  EX_so4_e : 0.096928
  EX_k_e : 0.075132
  EX_fe2_e : 0.006182
  EX_mg2_e : 0.003339
  EX_ca2_e : 0.002003
  EX_cl_e : 0.002003
  EX_cu2_e : 0.000273
  EX_mn2_e : 0.000266
  EX_zn2_e : 0.000131
  EX_ni2_e : 0.000124

Product: (mmol/gDw/h)
  EX_h2o_e : 52.583192
  EX_co2_e : 35.180217
  EX_h_e : 6.872362
  Auxiliary production reaction : 1.190605
  EX_glyclt_e : 0.687922
  EX_ac_e : 0.224089
  EX_hxan_e : 0.010072
  EX_ade_e : 0.000431
  DM_5drib_c : 0.000258
  DM_4crsol_c : 0.000086

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