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 (60 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 52
  Gene deletion: b2836 b3553 b1478 b1241 b0351 b4069 b4384 b3708 b3752 b3115 b1849 b2296 b2926 b2407 b3844 b1238 b1004 b3713 b1109 b0046 b3236 b0120 b0937 b1982 b2797 b3117 b1814 b4471 b1033 b0261 b0411 b2799 b3945 b1602 b0507 b3709 b2913 b4381 b2406 b3161 b0112 b1539 b2492 b0904 b1533 b1380 b1473 b4141 b1798 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.377905 (mmol/gDw/h)
  Minimum Production Rate : 0.066303 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.457942
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.043083
  EX_pi_e : 0.563439
  EX_so4_e : 0.161467
  EX_k_e : 0.073765
  EX_fe2_e : 0.006070
  EX_mg2_e : 0.003278
  EX_ca2_e : 0.001967
  EX_cl_e : 0.001967
  EX_cu2_e : 0.000268
  EX_mn2_e : 0.000261
  EX_zn2_e : 0.000129
  EX_ni2_e : 0.000122

Product: (mmol/gDw/h)
  EX_h2o_e : 51.632260
  EX_co2_e : 34.766127
  EX_h_e : 7.803853
  EX_ac_e : 1.568679
  EX_gsn_e : 0.499100
  Auxiliary production reaction : 0.066303
  EX_ade_e : 0.000423
  DM_5drib_c : 0.000254
  DM_4crsol_c : 0.000084

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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