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 : bwco1gdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (92 of 96: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 50
  Gene deletion: b4467 b1478 b4382 b3942 b1732 b1241 b4069 b4384 b3708 b2297 b2458 b2779 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b2920 b1982 b2797 b3117 b1814 b4471 b3551 b0261 b1701 b1805 b2799 b3945 b1602 b4219 b1832 b1778 b2406 b3915 b0728 b2366 b2492 b0904 b1533 b1380 b1710 b2480 b3662 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.384794 (mmol/gDw/h)
  Minimum Production Rate : 0.140695 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.727477
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.267891
  EX_pi_e : 0.793259
  EX_so4_e : 0.659679
  EX_tungs_e : 0.140695
  EX_k_e : 0.075109
  EX_fe3_e : 0.006182
  EX_mg2_e : 0.003338
  EX_ca2_e : 0.002003
  EX_cl_e : 0.002003
  EX_cu2_e : 0.000273
  EX_mn2_e : 0.000266
  EX_zn2_e : 0.000131
  EX_ni2_e : 0.000124

Product: (mmol/gDw/h)
  EX_h2o_e : 54.761210
  EX_co2_e : 38.408497
  EX_h_e : 4.752435
  EX_ac_e : 0.786802
  Auxiliary production reaction : 0.140695
  EX_hxan_e : 0.000431
  DM_5drib_c : 0.000258
  DM_4crsol_c : 0.000086

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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