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 : eig3p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (45 of 89: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3708 b3752 b2297 b2458 b2926 b3617 b2407 b1982 b2797 b3117 b1814 b4471 b2406 b0112 b2868 b0114 b1539 b2492 b0904 b1533 b3662 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.393909 (mmol/gDw/h)
  Minimum Production Rate : 1.179253 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.689725
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.614015
  EX_pi_e : 1.559220
  EX_so4_e : 0.099194
  EX_k_e : 0.076888
  EX_fe2_e : 0.006327
  EX_mg2_e : 0.003417
  EX_ca2_e : 0.002050
  EX_cl_e : 0.002050
  EX_cu2_e : 0.000279
  EX_mn2_e : 0.000272
  EX_zn2_e : 0.000134
  EX_ni2_e : 0.000127

Product: (mmol/gDw/h)
  EX_h2o_e : 51.241008
  EX_co2_e : 34.940046
  EX_h_e : 6.886262
  Auxiliary production reaction : 1.179253
  EX_ac_e : 0.907038
  EX_ade_e : 0.000265
  DM_mththf_c : 0.000176
  DM_5drib_c : 0.000089
  DM_4crsol_c : 0.000088

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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