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 : forcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b0474 b2518 b1241 b0351 b3831 b4384 b3708 b3008 b0910 b3752 b0871 b3617 b2407 b1982 b2797 b3117 b1814 b4471 b0261 b4381 b2406 b2943 b0837 b0124 b0114 b2366 b2492 b0904 b1533 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.612032 (mmol/gDw/h)
  Minimum Production Rate : 0.227389 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.332278
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.877958
  EX_pi_e : 1.272538
  EX_so4_e : 0.381511
  EX_k_e : 0.119464
  EX_fe2_e : 0.009830
  EX_mg2_e : 0.005309
  EX_ca2_e : 0.003186
  EX_cl_e : 0.003186
  EX_cu2_e : 0.000434
  EX_mn2_e : 0.000423
  EX_zn2_e : 0.000209
  EX_ni2_e : 0.000198
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 47.568754
  EX_co2_e : 25.168047
  EX_h_e : 6.982101
  EX_acald_e : 1.508036
  EX_thym_e : 0.338169
  Auxiliary production reaction : 0.227389
  DM_5drib_c : 0.000411
  DM_4crsol_c : 0.000136

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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