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 : ppcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (93 of 117: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4069 b4384 b3708 b3008 b3752 b2297 b2458 b2925 b2097 b2407 b1238 b3236 b1779 b1982 b2797 b3117 b1814 b4471 b3946 b2210 b0825 b0595 b0261 b0507 b4381 b2406 b0114 b1539 b2492 b0904 b2578 b1533 b3927 b2835 b0494 b0516 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.596640 (mmol/gDw/h)
  Minimum Production Rate : 0.151641 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 26.750848
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.507816
  EX_pi_e : 1.030445
  EX_so4_e : 0.301887
  EX_k_e : 0.116460
  EX_fe2_e : 0.009583
  EX_mg2_e : 0.005176
  EX_ca2_e : 0.003106
  EX_cl_e : 0.003106
  EX_cu2_e : 0.000423
  EX_mn2_e : 0.000412
  EX_zn2_e : 0.000203
  EX_ni2_e : 0.000193
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 47.042780
  EX_co2_e : 28.249681
  EX_h_e : 7.748565
  EX_ac_e : 1.808807
  Auxiliary production reaction : 0.151641
  EX_alltn_e : 0.000668
  DM_5drib_c : 0.000400
  DM_4crsol_c : 0.000133

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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