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 : ahcys_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b4467 b4382 b4069 b4384 b3708 b3008 b3752 b3926 b3115 b1849 b2296 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b2687 b1982 b4139 b2797 b3117 b1814 b4471 b1602 b2406 b0114 b2366 b2492 b0904 b1533 b3927 b3029 b3821 b1380 b2660 b4141 b1798 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.483385 (mmol/gDw/h)
  Minimum Production Rate : 0.153787 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.180008
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.143234
  EX_pi_e : 0.466276
  EX_so4_e : 0.275513
  EX_k_e : 0.094353
  EX_fe2_e : 0.007764
  EX_mg2_e : 0.004193
  EX_ca2_e : 0.002516
  EX_cl_e : 0.002516
  EX_cu2_e : 0.000343
  EX_mn2_e : 0.000334
  EX_zn2_e : 0.000165
  EX_ni2_e : 0.000156
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.052642
  EX_co2_e : 37.134775
  EX_h_e : 5.491885
  EX_ac_e : 0.435207
  Auxiliary production reaction : 0.153787
  DM_5drib_c : 0.000324
  DM_4crsol_c : 0.000108

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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