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 : pnto__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (24 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b2836 b3831 b4384 b3708 b3008 b0871 b2925 b2097 b0030 b2407 b2797 b3117 b1814 b4471 b3946 b0825 b3665 b4381 b2406 b3654 b3714 b3664 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b2413 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.767979 (mmol/gDw/h)
  Minimum Production Rate : 0.144284 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.428889
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.567378
  EX_pi_e : 0.740798
  EX_so4_e : 0.322374
  EX_k_e : 0.149904
  EX_fe2_e : 0.012335
  EX_mg2_e : 0.006662
  EX_ca2_e : 0.003997
  EX_cl_e : 0.003997
  EX_cu2_e : 0.000544
  EX_mn2_e : 0.000531
  EX_zn2_e : 0.000262
  EX_ni2_e : 0.000248
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 47.361254
  EX_co2_e : 26.534510
  EX_h_e : 7.216088
  Auxiliary production reaction : 0.144284
  EX_met__L_e : 0.128981
  DM_5drib_c : 0.000173
  DM_4crsol_c : 0.000171

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