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 : 2dr5p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3942 b1732 b3708 b0871 b2297 b2458 b2779 b2925 b2097 b3236 b2690 b2797 b3117 b1814 b4471 b2210 b3945 b4381 b2868 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b1813 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.366553 (mmol/gDw/h)
  Minimum Production Rate : 0.253887 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.827054
  EX_glc__D_e : 10.000000
  EX_nh4_e : 3.958747
  EX_pi_e : 0.607466
  EX_so4_e : 0.092305
  EX_k_e : 0.071549
  EX_fe2_e : 0.005887
  EX_mg2_e : 0.003180
  EX_ca2_e : 0.001908
  EX_cl_e : 0.001908
  EX_cu2_e : 0.000260
  EX_mn2_e : 0.000253
  EX_zn2_e : 0.000125
  EX_ni2_e : 0.000118

Product: (mmol/gDw/h)
  EX_h2o_e : 43.259458
  EX_co2_e : 28.146430
  EX_h_e : 8.547640
  EX_pyr_e : 5.179477
  Auxiliary production reaction : 0.253887
  EX_glyc__R_e : 0.000123
  DM_5drib_c : 0.000082
  DM_4crsol_c : 0.000082

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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