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 : prbamp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (35 of 47: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b3399 b3831 b4069 b4384 b2744 b3708 b3008 b0910 b3115 b1849 b2296 b2926 b2407 b1982 b2797 b3117 b1814 b4471 b2440 b4374 b0675 b2361 b2291 b0261 b2239 b0114 b2366 b2492 b0904 b2578 b1533 b3927 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.470191 (mmol/gDw/h)
  Minimum Production Rate : 0.199172 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.402551
  EX_o2_e : 286.657267
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.073879
  EX_pi_e : 0.851892
  EX_so4_e : 0.118403
  EX_k_e : 0.091778
  EX_mg2_e : 0.004079
  EX_ca2_e : 0.002447
  EX_cl_e : 0.002447
  EX_cu2_e : 0.000333
  EX_mn2_e : 0.000325
  EX_zn2_e : 0.000160
  EX_ni2_e : 0.000152
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992448
  EX_h2o_e : 552.365793
  EX_co2_e : 37.164728
  EX_ac_e : 0.273739
  Auxiliary production reaction : 0.199172
  DM_5drib_c : 0.000315
  DM_4crsol_c : 0.000105

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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