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 : 14dhncoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (53 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b3553 b4384 b3708 b3008 b0871 b2779 b0030 b2407 b1238 b0583 b1982 b2797 b3117 b1814 b4471 b1033 b0261 b3709 b4381 b2406 b3161 b0112 b2789 b3127 b0114 b0886 b2366 b0755 b3612 b2492 b0904 b2578 b1533 b3927 b2835 b1473 b0494 b1600 b0514 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.669862 (mmol/gDw/h)
  Minimum Production Rate : 0.092254 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.029318
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.880986
  EX_pi_e : 0.922916
  EX_so4_e : 0.260939
  EX_k_e : 0.130752
  EX_fe2_e : 0.010759
  EX_mg2_e : 0.005811
  EX_ca2_e : 0.003487
  EX_cl_e : 0.003487
  EX_cu2_e : 0.000475
  EX_mn2_e : 0.000463
  EX_zn2_e : 0.000228
  EX_ni2_e : 0.000216
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 49.731675
  EX_co2_e : 29.550098
  EX_h_e : 6.433225
  Auxiliary production reaction : 0.092254
  DM_oxam_c : 0.000750
  DM_5drib_c : 0.000449
  DM_4crsol_c : 0.000149

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