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 (70 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 55
  Gene deletion: b3553 b1478 b1241 b4069 b4384 b2744 b3708 b3115 b1849 b2296 b2926 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b0937 b2797 b3117 b1814 b4471 b1033 b3665 b4374 b2361 b2291 b0261 b0411 b2799 b3945 b1602 b3709 b3161 b0112 b3654 b3714 b3664 b1539 b2492 b0904 b1533 b3825 b1380 b1473 b0494 b2660 b4141 b1798 b3662 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.349824 (mmol/gDw/h)
  Minimum Production Rate : 0.266476 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.920461
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.643401
  EX_pi_e : 1.136871
  EX_so4_e : 0.354569
  EX_k_e : 0.068283
  EX_fe2_e : 0.005619
  EX_mg2_e : 0.003035
  EX_ca2_e : 0.001821
  EX_cl_e : 0.001821
  EX_cu2_e : 0.000248
  EX_mn2_e : 0.000242
  EX_zn2_e : 0.000119
  EX_ni2_e : 0.000113

Product: (mmol/gDw/h)
  EX_h2o_e : 51.366206
  EX_co2_e : 34.933468
  EX_h_e : 5.104065
  EX_ac_e : 1.090316
  Auxiliary production reaction : 0.266476
  DM_5drib_c : 0.000079
  DM_4crsol_c : 0.000078

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