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 (20 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b2836 b4382 b0586 b4384 b2744 b3708 b3008 b0871 b2407 b2797 b3117 b1814 b4471 b0261 b3709 b2406 b3161 b0112 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b1473 b4141 b1798 b3662 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.558764 (mmol/gDw/h)
  Minimum Production Rate : 0.077302 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.320846
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.575715
  EX_pi_e : 0.770892
  EX_so4_e : 0.218010
  EX_k_e : 0.109067
  EX_mg2_e : 0.004847
  EX_fe2_e : 0.004611
  EX_fe3_e : 0.004363
  EX_ca2_e : 0.002908
  EX_cl_e : 0.002908
  EX_cu2_e : 0.000396
  EX_mn2_e : 0.000386
  EX_zn2_e : 0.000191
  EX_ni2_e : 0.000180
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 51.432028
  EX_co2_e : 34.591652
  EX_h_e : 5.370414
  Auxiliary production reaction : 0.077302
  DM_5drib_c : 0.000126
  DM_4crsol_c : 0.000125

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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