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 (20 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b2836 b3399 b1241 b0351 b4069 b2744 b3708 b2297 b2458 b3617 b1238 b2883 b2797 b3117 b1814 b4471 b1623 b3665 b0261 b0411 b4381 b2406 b0112 b3654 b3714 b3664 b0114 b2366 b2492 b0904 b1533 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.545340 (mmol/gDw/h)
  Minimum Production Rate : 1.633041 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 17.611209
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.522668
  EX_pi_e : 0.526038
  EX_so4_e : 0.137328
  EX_k_e : 0.106447
  EX_fe2_e : 0.008759
  EX_mg2_e : 0.004731
  EX_ca2_e : 0.002838
  EX_cl_e : 0.002838
  EX_cu2_e : 0.000387
  EX_mn2_e : 0.000377
  EX_zn2_e : 0.000186
  EX_ni2_e : 0.000176
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 38.075024
  EX_co2_e : 20.408018
  EX_h_e : 9.532338
  Auxiliary production reaction : 1.633041
  EX_ac_e : 1.255453
  DM_5drib_c : 0.000123
  DM_4crsol_c : 0.000122

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.

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Last updated: 21-Sep-2023
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