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 : duri_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (30 of 50: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4382 b3942 b1732 b1241 b0351 b4069 b4384 b2744 b3752 b0871 b2297 b2458 b2779 b2925 b2097 b2926 b2407 b3236 b3616 b3589 b3946 b2210 b0825 b3665 b3654 b3714 b3664 b0114 b0529 b2492 b0904 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.284481 (mmol/gDw/h)
  Minimum Production Rate : 1.091166 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.774313
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.254704
  EX_pi_e : 0.274412
  EX_so4_e : 0.071638
  EX_k_e : 0.055529
  EX_fe2_e : 0.004569
  EX_mg2_e : 0.002468
  EX_ca2_e : 0.001481
  EX_cl_e : 0.001481
  EX_cu2_e : 0.000202
  EX_mn2_e : 0.000197
  EX_zn2_e : 0.000097
  EX_ni2_e : 0.000092

Product: (mmol/gDw/h)
  EX_h2o_e : 44.047404
  EX_co2_e : 26.592425
  EX_h_e : 9.053347
  EX_pyr_e : 3.395624
  Auxiliary production reaction : 1.091166
  EX_ac_e : 0.861465
  DM_mththf_c : 0.000127
  DM_5drib_c : 0.000064
  DM_4crsol_c : 0.000063

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