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 (72 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b3553 b4069 b4384 b3708 b3008 b3115 b1849 b2296 b0030 b2407 b3844 b1238 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b2797 b3117 b1814 b4471 b1033 b0261 b2799 b3945 b1602 b0153 b2913 b4381 b2406 b1727 b0114 b1539 b2492 b0904 b0591 b1533 b3927 b3825 b1380 b0494 b4141 b1798 b3662 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.438543 (mmol/gDw/h)
  Minimum Production Rate : 0.612216 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.264112
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.350408
  EX_pi_e : 0.423021
  EX_so4_e : 0.110434
  EX_k_e : 0.085601
  EX_fe2_e : 0.007043
  EX_mg2_e : 0.003804
  EX_ca2_e : 0.002283
  EX_cl_e : 0.002283
  EX_cu2_e : 0.000311
  EX_mn2_e : 0.000303
  EX_zn2_e : 0.000150
  EX_ni2_e : 0.000142
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 48.620621
  EX_co2_e : 35.865977
  EX_h_e : 5.511218
  Auxiliary production reaction : 0.612216
  EX_ac_e : 0.255314
  EX_etoh_e : 0.054919
  EX_hxan_e : 0.000491
  DM_5drib_c : 0.000294
  DM_4crsol_c : 0.000098

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