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 : hxan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b4467 b4069 b3926 b0512 b2297 b2458 b1004 b3713 b1109 b0046 b3236 b1638 b4139 b1602 b2913 b4381 b3654 b3714 b3664 b4064 b4464 b0114 b0529 b2492 b0904 b3029 b1380 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.493073 (mmol/gDw/h)
  Minimum Production Rate : 0.228175 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.563719
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.237849
  EX_pi_e : 0.475621
  EX_so4_e : 0.124166
  EX_k_e : 0.096244
  EX_fe2_e : 0.007919
  EX_mg2_e : 0.004277
  EX_cl_e : 0.002566
  EX_ca2_e : 0.002566
  EX_cu2_e : 0.000350
  EX_mn2_e : 0.000341
  EX_zn2_e : 0.000168
  EX_ni2_e : 0.000159
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 53.119785
  EX_co2_e : 38.045510
  EX_h_e : 5.730314
  EX_ac_e : 0.287060
  Auxiliary production reaction : 0.228175
  DM_mththf_c : 0.000221
  DM_5drib_c : 0.000111
  DM_4crsol_c : 0.000110

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