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 : dimp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b1241 b0351 b4384 b2744 b2930 b4232 b3697 b3925 b0871 b3115 b1849 b2296 b2779 b3617 b2407 b3946 b0825 b4381 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b0529 b2492 b0904 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.421011 (mmol/gDw/h)
  Minimum Production Rate : 0.249846 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.443910
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.546270
  EX_pi_e : 0.655956
  EX_so4_e : 0.106019
  EX_k_e : 0.082178
  EX_fe2_e : 0.006762
  EX_mg2_e : 0.003652
  EX_ca2_e : 0.002191
  EX_cl_e : 0.002191
  EX_cu2_e : 0.000298
  EX_mn2_e : 0.000291
  EX_zn2_e : 0.000144
  EX_ni2_e : 0.000136
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 45.784233
  EX_co2_e : 27.767007
  EX_h_e : 9.019121
  EX_pyr_e : 4.151177
  Auxiliary production reaction : 0.249846
  EX_glyc__R_e : 0.000141
  DM_5drib_c : 0.000095
  DM_4crsol_c : 0.000094

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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