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 : accoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 51
  Gene deletion: b3553 b1478 b1241 b4069 b4384 b2744 b1278 b3708 b3614 b0910 b3752 b2297 b2458 b2926 b2781 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1759 b1982 b2797 b3117 b1814 b4471 b1033 b4374 b0675 b0261 b0411 b2799 b3945 b1602 b4381 b2406 b3915 b0452 b1539 b2492 b0904 b1533 b1380 b3918 b2660 b4141 b1798 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.434421 (mmol/gDw/h)
  Minimum Production Rate : 0.141313 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.371122
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.683328
  EX_pi_e : 0.842982
  EX_so4_e : 0.250709
  EX_k_e : 0.084796
  EX_fe3_e : 0.006979
  EX_mg2_e : 0.003769
  EX_ca2_e : 0.002261
  EX_cl_e : 0.002261
  EX_cu2_e : 0.000308
  EX_mn2_e : 0.000300
  EX_zn2_e : 0.000148
  EX_ni2_e : 0.000140
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 51.739605
  EX_co2_e : 37.440126
  EX_h_e : 5.052624
  EX_ac_e : 0.407629
  EX_3hpp_e : 0.220014
  Auxiliary production reaction : 0.141312
  EX_ade_e : 0.000486
  DM_5drib_c : 0.000291
  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 (2023).
[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: 09-Jul-2025
Contact