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 : pnto__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (45 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3399 b4382 b1241 b0351 b3831 b4069 b2744 b3708 b0871 b3115 b1849 b2296 b2925 b2097 b0160 b2690 b2797 b3117 b1814 b4471 b2498 b3616 b3589 b2361 b2291 b0261 b3945 b2406 b2868 b0114 b2366 b2492 b0904 b1533 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.461990 (mmol/gDw/h)
  Minimum Production Rate : 0.995723 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.191649
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.760695
  EX_pi_e : 0.445638
  EX_so4_e : 0.116338
  EX_k_e : 0.090177
  EX_fe2_e : 0.007420
  EX_mg2_e : 0.004008
  EX_cl_e : 0.002405
  EX_ca2_e : 0.002405
  EX_cu2_e : 0.000328
  EX_mn2_e : 0.000319
  EX_zn2_e : 0.000158
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 44.528025
  EX_co2_e : 28.591783
  EX_h_e : 8.269288
  EX_ac_e : 1.257374
  Auxiliary production reaction : 0.995723
  EX_xan_e : 0.193569
  EX_hxan_e : 0.000311
  DM_5drib_c : 0.000104
  DM_4crsol_c : 0.000103

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