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 : malcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (81 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 60
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b3708 b1479 b2297 b2458 b2925 b2097 b3617 b0160 b1238 b3124 b3236 b1779 b3962 b1982 b0104 b2797 b3117 b1814 b4471 b3946 b0825 b4267 b0675 b2361 b1415 b1014 b0261 b0822 b2799 b3709 b2913 b4381 b2406 b3161 b0112 b2789 b3127 b0452 b2868 b2975 b0114 b3603 b0509 b3125 b0755 b3612 b1539 b2492 b0904 b1533 b1380 b1473 b0594 b4266 b0221   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.257861 (mmol/gDw/h)
  Minimum Production Rate : 0.273630 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.775670
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.926091
  EX_pi_e : 1.069626
  EX_so4_e : 0.562922
  EX_k_e : 0.050333
  EX_fe2_e : 0.004142
  EX_mg2_e : 0.002237
  EX_ca2_e : 0.001342
  EX_cl_e : 0.001342
  EX_cu2_e : 0.000183
  EX_mn2_e : 0.000178
  EX_zn2_e : 0.000088
  EX_ni2_e : 0.000083

Product: (mmol/gDw/h)
  EX_h2o_e : 43.893331
  EX_co2_e : 30.886094
  EX_h_e : 8.660158
  EX_ac_e : 5.419048
  Auxiliary production reaction : 0.273630
  EX_met__L_e : 0.224357
  EX_ade_e : 0.000289
  DM_5drib_c : 0.000173
  EX_dxylnt_e : 0.000173
  DM_4crsol_c : 0.000058

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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