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 : alltn_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (88 of 90: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b4467 b1478 b4269 b0493 b3846 b3588 b3003 b3011 b0238 b0125 b1241 b0351 b0871 b3617 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b0477 b4139 b4015 b2799 b3945 b1602 b4381 b3915 b3654 b3714 b3664 b4064 b4464 b2492 b0904 b2954 b3029 b1380 b1301 b2660 b0515 b1518 b0221 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.491631 (mmol/gDw/h)
  Minimum Production Rate : 0.016291 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.409748
  EX_o2_e : 286.666923
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.374625
  EX_pi_e : 0.474230
  EX_so4_e : 0.123804
  EX_k_e : 0.095963
  EX_mg2_e : 0.004265
  EX_ca2_e : 0.002559
  EX_cl_e : 0.002559
  EX_cu2_e : 0.000349
  EX_mn2_e : 0.000340
  EX_zn2_e : 0.000168
  EX_ni2_e : 0.000159
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992102
  EX_h2o_e : 551.178849
  EX_co2_e : 38.086340
  EX_acald_e : 0.834154
  EX_alltn_e : 0.016263
  DM_mththf_c : 0.000220
  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