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 (40 of 89: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b0871 b2779 b3617 b0030 b2883 b0907 b1982 b1623 b0261 b0411 b4381 b0112 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.511512 (mmol/gDw/h)
  Minimum Production Rate : 1.636036 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 25.749794
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.796361
  EX_pi_e : 2.129444
  EX_so4_e : 0.128809
  EX_k_e : 0.099844
  EX_fe2_e : 0.008215
  EX_mg2_e : 0.004437
  EX_ca2_e : 0.002662
  EX_cl_e : 0.002662
  EX_cu2_e : 0.000363
  EX_mn2_e : 0.000353
  EX_zn2_e : 0.000174
  EX_ni2_e : 0.000165
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 48.344062
  EX_co2_e : 26.656257
  EX_h_e : 7.972051
  Auxiliary production reaction : 1.636036
  EX_acald_e : 1.265578
  DM_5drib_c : 0.000343
  DM_4crsol_c : 0.000114

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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