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 : imp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (42 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3399 b0238 b0125 b1241 b0351 b4069 b4384 b2744 b3115 b1849 b2296 b3617 b0030 b2883 b1982 b0477 b1623 b4374 b2361 b2291 b0261 b0411 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.584968 (mmol/gDw/h)
  Minimum Production Rate : 1.121076 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 22.378670
  EX_nh4_e : 10.801912
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.685340
  EX_so4_e : 0.147307
  EX_k_e : 0.114182
  EX_fe2_e : 0.009395
  EX_mg2_e : 0.005075
  EX_ca2_e : 0.003045
  EX_cl_e : 0.003045
  EX_cu2_e : 0.000415
  EX_mn2_e : 0.000404
  EX_zn2_e : 0.000199
  EX_ni2_e : 0.000189
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 48.603677
  EX_co2_e : 20.824444
  EX_h_e : 11.835841
  EX_ac_e : 1.976615
  Auxiliary production reaction : 1.121076
  DM_5drib_c : 0.000393
  DM_4crsol_c : 0.000130

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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