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 : succoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (27 of 28: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 54
  Gene deletion: b4467 b1478 b3399 b1241 b4069 b2744 b3708 b2930 b4232 b3697 b3925 b3115 b1849 b2296 b2779 b3844 b1238 b1004 b3713 b1109 b0046 b3236 b0937 b1982 b2797 b3117 b1814 b4471 b3946 b2210 b0825 b0675 b2361 b0261 b2799 b3945 b1602 b0507 b4381 b2406 b0452 b2975 b3603 b1539 b2492 b0904 b1533 b1380 b2660 b4141 b1798 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.332283 (mmol/gDw/h)
  Minimum Production Rate : 0.185139 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.059928
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.886458
  EX_pi_e : 0.875939
  EX_so4_e : 0.268814
  EX_k_e : 0.064859
  EX_fe2_e : 0.005337
  EX_mg2_e : 0.002883
  EX_ca2_e : 0.001730
  EX_cl_e : 0.001730
  EX_cu2_e : 0.000236
  EX_mn2_e : 0.000230
  EX_zn2_e : 0.000113
  EX_ni2_e : 0.000107

Product: (mmol/gDw/h)
  EX_h2o_e : 44.527046
  EX_co2_e : 31.860741
  EX_h_e : 8.730314
  EX_ac_e : 4.934752
  Auxiliary production reaction : 0.185139
  EX_ade_e : 0.000372
  DM_5drib_c : 0.000223
  DM_4crsol_c : 0.000074

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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