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 : 2dr1p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (37 of 40: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b4069 b2744 b3708 b3115 b1849 b2296 b2925 b2097 b3236 b2690 b2797 b3117 b1814 b4471 b2210 b3945 b2913 b4381 b2868 b4064 b4464 b0114 b0755 b3612 b1539 b2492 b0904 b1533 b3927 b2835 b0494 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.401384 (mmol/gDw/h)
  Minimum Production Rate : 0.119979 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.903826
  EX_o2_e : 281.986571
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.856833
  EX_pi_e : 0.507156
  EX_so4_e : 0.101076
  EX_k_e : 0.078347
  EX_mg2_e : 0.003482
  EX_cl_e : 0.002089
  EX_ca2_e : 0.002089
  EX_cu2_e : 0.000285
  EX_mn2_e : 0.000277
  EX_zn2_e : 0.000137
  EX_ni2_e : 0.000130
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993553
  EX_h2o_e : 544.403805
  EX_co2_e : 32.513289
  EX_ac_e : 4.879730
  EX_xan_e : 0.130481
  Auxiliary production reaction : 0.119979
  DM_5drib_c : 0.000090
  DM_4crsol_c : 0.000090

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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