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 : fprica_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3399 b0474 b2518 b2744 b3708 b3008 b0871 b0160 b1779 b1982 b2797 b3117 b1814 b4471 b2440 b0675 b2361 b0261 b4381 b2868 b0114 b0886 b2366 b0529 b2492 b0904 b1533 b3927   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.692258 (mmol/gDw/h)
  Minimum Production Rate : 0.141093 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.013100
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.115485
  EX_pi_e : 0.808849
  EX_so4_e : 0.174324
  EX_k_e : 0.135124
  EX_fe2_e : 0.011118
  EX_mg2_e : 0.006005
  EX_ca2_e : 0.003603
  EX_cl_e : 0.003603
  EX_cu2_e : 0.000491
  EX_mn2_e : 0.000478
  EX_zn2_e : 0.000236
  EX_ni2_e : 0.000224
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 49.941390
  EX_co2_e : 30.082156
  EX_h_e : 6.999900
  Auxiliary production reaction : 0.141093
  EX_xan_e : 0.018114
  EX_ade_e : 0.000466
  DM_5drib_c : 0.000156
  DM_4crsol_c : 0.000154

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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