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 : dcyt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (16 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b0871 b3617 b1238 b2883 b1982 b0675 b2361 b0261 b4381 b0112 b4064 b4464 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.558981 (mmol/gDw/h)
  Minimum Production Rate : 1.325013 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 20.587121
  EX_nh4_e : 10.996180
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.539196
  EX_so4_e : 0.140762
  EX_k_e : 0.109109
  EX_fe2_e : 0.008978
  EX_mg2_e : 0.004849
  EX_ca2_e : 0.002909
  EX_cl_e : 0.002909
  EX_cu2_e : 0.000396
  EX_mn2_e : 0.000386
  EX_zn2_e : 0.000191
  EX_ni2_e : 0.000181
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 47.197877
  EX_co2_e : 20.209059
  EX_h_e : 10.095374
  Auxiliary production reaction : 1.325013
  EX_thymd_e : 0.492100
  DM_5drib_c : 0.000375
  DM_4crsol_c : 0.000125

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