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 : 14dhncoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (15 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b1241 b0351 b4069 b4384 b3708 b3115 b1849 b2296 b3617 b0030 b2407 b1238 b2797 b3117 b1814 b4471 b0595 b3665 b0261 b3709 b4381 b2406 b3161 b0112 b0452 b3654 b3714 b3664 b0114 b1539 b2492 b0904 b1533 b1473 b4141 b1798 b3662 b0221   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.390422 (mmol/gDw/h)
  Minimum Production Rate : 0.584582 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 18.545612
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.308598
  EX_pi_e : 2.130350
  EX_so4_e : 0.682898
  EX_k_e : 0.076208
  EX_fe2_e : 0.006271
  EX_mg2_e : 0.003387
  EX_ca2_e : 0.002032
  EX_cl_e : 0.002032
  EX_cu2_e : 0.000277
  EX_mn2_e : 0.000270
  EX_zn2_e : 0.000133
  EX_ni2_e : 0.000126

Product: (mmol/gDw/h)
  EX_h2o_e : 46.057043
  EX_co2_e : 19.963363
  EX_h_e : 7.993590
  EX_ac_e : 2.652492
  Auxiliary production reaction : 0.584582
  DM_5drib_c : 0.000088
  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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