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 : gdpofuc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (58 of 71: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b4467 b4069 b4384 b3752 b2297 b2458 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b1982 b4139 b1623 b0261 b2799 b3945 b1602 b4381 b2406 b3915 b1727 b2975 b0114 b3603 b0509 b3125 b0755 b3612 b0529 b2492 b0904 b2954 b3029 b1380 b0508 b2660 b1695 b3662 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.434896 (mmol/gDw/h)
  Minimum Production Rate : 0.267228 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.638340
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.034923
  EX_pi_e : 0.953959
  EX_so4_e : 0.109515
  EX_k_e : 0.084889
  EX_fe3_e : 0.006985
  EX_mg2_e : 0.003773
  EX_ca2_e : 0.002264
  EX_cl_e : 0.002264
  EX_cu2_e : 0.000308
  EX_mn2_e : 0.000301
  EX_zn2_e : 0.000148
  EX_ni2_e : 0.000140
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.259059
  EX_co2_e : 36.964939
  EX_h_e : 5.059801
  Auxiliary production reaction : 0.267228
  EX_ac_e : 0.253190
  EX_etoh_e : 0.199579
  EX_hxan_e : 0.000487
  DM_5drib_c : 0.000292
  DM_4crsol_c : 0.000097

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