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 : accoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (49 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b0586 b1241 b0351 b4069 b4384 b3708 b3115 b1849 b2296 b2779 b2926 b0030 b2407 b1238 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b0261 b3709 b2913 b4381 b2406 b3161 b0112 b2789 b3127 b2975 b0114 b3603 b1539 b2492 b0904 b1533 b3821 b1473 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.388081 (mmol/gDw/h)
  Minimum Production Rate : 0.580642 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.034362
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.256168
  EX_pi_e : 2.116272
  EX_so4_e : 0.678369
  EX_k_e : 0.075751
  EX_fe2_e : 0.006233
  EX_mg2_e : 0.003367
  EX_ca2_e : 0.002020
  EX_cl_e : 0.002020
  EX_cu2_e : 0.000275
  EX_mn2_e : 0.000268
  EX_zn2_e : 0.000132
  EX_ni2_e : 0.000125

Product: (mmol/gDw/h)
  EX_h2o_e : 47.304463
  EX_co2_e : 25.442612
  EX_h_e : 7.944612
  EX_ac_e : 2.635977
  Auxiliary production reaction : 0.580642
  DM_oxam_c : 0.000434
  DM_5drib_c : 0.000260
  DM_4crsol_c : 0.000087

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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