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 : mmcoa__S_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (16 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4384 b3708 b3008 b3752 b0871 b2779 b2407 b2797 b3117 b1814 b4471 b3665 b4381 b2406 b3654 b3714 b3664 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b3821 b4141 b1798 b3662 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.687852 (mmol/gDw/h)
  Minimum Production Rate : 0.079379 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.273228
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.984399
  EX_pi_e : 0.901644
  EX_so4_e : 0.252594
  EX_k_e : 0.134264
  EX_fe2_e : 0.011048
  EX_mg2_e : 0.005967
  EX_ca2_e : 0.003580
  EX_cl_e : 0.003580
  EX_cu2_e : 0.000488
  EX_mn2_e : 0.000475
  EX_zn2_e : 0.000235
  EX_ni2_e : 0.000222
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 49.612046
  EX_co2_e : 29.780808
  EX_h_e : 6.637777
  Auxiliary production reaction : 0.079379
  DM_mththf_c : 0.000308
  DM_5drib_c : 0.000155
  DM_4crsol_c : 0.000153

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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