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 : ppcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 117: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b2836 b4384 b2744 b3708 b3008 b3752 b0871 b2883 b1779 b1982 b2797 b3117 b1814 b4471 b0261 b4381 b2406 b2868 b4064 b4464 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b4141 b1798 b3662 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.684043 (mmol/gDw/h)
  Minimum Production Rate : 0.078337 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.459477
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.939794
  EX_pi_e : 0.894844
  EX_so4_e : 0.250593
  EX_k_e : 0.133520
  EX_fe3_e : 0.010986
  EX_mg2_e : 0.005934
  EX_ca2_e : 0.003560
  EX_cl_e : 0.003560
  EX_cu2_e : 0.000485
  EX_mn2_e : 0.000473
  EX_zn2_e : 0.000233
  EX_ni2_e : 0.000221
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 49.670321
  EX_co2_e : 30.037731
  EX_h_e : 6.535085
  Auxiliary production reaction : 0.078337
  EX_ade_e : 0.000765
  DM_5drib_c : 0.000459
  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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