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 : nad_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b4467 b4069 b4384 b3708 b3752 b3115 b1849 b2296 b2407 b1004 b3713 b1109 b0046 b3124 b3236 b1779 b1982 b2797 b3117 b1814 b4471 b0261 b1602 b2913 b4381 b2406 b3915 b1727 b2975 b0114 b3603 b2366 b0529 b2492 b0904 b1533 b3927 b3821 b1380 b0514 b1771 b3662 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.451369 (mmol/gDw/h)
  Minimum Production Rate : 0.191199 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.427003
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.215156
  EX_pi_e : 0.817790
  EX_so4_e : 0.113664
  EX_k_e : 0.088104
  EX_fe3_e : 0.007249
  EX_mg2_e : 0.003916
  EX_ca2_e : 0.002349
  EX_cl_e : 0.002349
  EX_cu2_e : 0.000320
  EX_mn2_e : 0.000312
  EX_zn2_e : 0.000154
  EX_ni2_e : 0.000146
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.752782
  EX_co2_e : 36.817288
  EX_h_e : 5.221479
  EX_ac_e : 0.262781
  Auxiliary production reaction : 0.191199
  EX_3hpp_e : 0.037277
  EX_hxan_e : 0.000505
  DM_5drib_c : 0.000303
  DM_4crsol_c : 0.000101

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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