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 : pnto__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b2836 b3553 b3399 b4069 b2744 b3708 b0871 b3115 b1849 b2296 b2925 b2097 b1004 b3713 b1109 b0046 b3236 b2883 b2797 b3117 b1814 b4471 b3946 b2210 b0825 b1033 b4374 b2361 b2291 b1602 b4381 b3654 b2868 b3714 b3664 b1727 b4064 b4464 b0114 b1539 b2492 b0904 b1533 b3927 b1380 b2660 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.393942 (mmol/gDw/h)
  Minimum Production Rate : 0.501322 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.547645
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.757189
  EX_pi_e : 0.379999
  EX_so4_e : 0.099203
  EX_k_e : 0.076895
  EX_fe2_e : 0.006327
  EX_mg2_e : 0.003417
  EX_ca2_e : 0.002050
  EX_cl_e : 0.002050
  EX_cu2_e : 0.000279
  EX_mn2_e : 0.000272
  EX_zn2_e : 0.000134
  EX_ni2_e : 0.000127

Product: (mmol/gDw/h)
  EX_h2o_e : 37.452983
  EX_co2_e : 28.780919
  EX_h_e : 5.164045
  EX_12ppd__R_e : 3.047449
  Auxiliary production reaction : 0.501322
  EX_pyr_e : 0.311030
  EX_ac_e : 0.229348
  EX_adn_e : 0.000265
  DM_mththf_c : 0.000176
  DM_5drib_c : 0.000089
  DM_4crsol_c : 0.000088

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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