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 : gdpmann_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (108 of 108: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 60
  Gene deletion: b2836 b3553 b1478 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3708 b3008 b3752 b0871 b2779 b2925 b2097 b3617 b2407 b1238 b1004 b3713 b1109 b0046 b3236 b1638 b0121 b1982 b4139 b2797 b3117 b1814 b4471 b3946 b0825 b1033 b1623 b0261 b2799 b3945 b1602 b2913 b4381 b2406 b3915 b0114 b0509 b3125 b2366 b2492 b0904 b1533 b3029 b1380 b4141 b1798 b3662 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.306032 (mmol/gDw/h)
  Minimum Production Rate : 0.005734 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.453113
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.513546
  EX_pi_e : 0.306669
  EX_so4_e : 0.077065
  EX_k_e : 0.059735
  EX_fe3_e : 0.004915
  EX_mg2_e : 0.002655
  EX_ca2_e : 0.001593
  EX_cl_e : 0.001593
  EX_cu2_e : 0.000217
  EX_mn2_e : 0.000211
  EX_zn2_e : 0.000104
  EX_ni2_e : 0.000099

Product: (mmol/gDw/h)
  EX_h2o_e : 44.607351
  EX_co2_e : 27.170982
  EX_h_e : 9.931051
  EX_pyr_e : 4.917234
  EX_his__L_e : 0.726128
  EX_acald_e : 0.532596
  Auxiliary production reaction : 0.005734
  EX_hxan_e : 0.000342
  DM_5drib_c : 0.000205
  DM_4crsol_c : 0.000068

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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