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 : 10fthf_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (46 of 46: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 76
  Gene deletion: b3553 b3399 b4269 b0493 b3846 b3588 b3003 b3011 b0474 b2518 b1241 b0351 b2744 b3708 b3008 b1479 b0871 b3115 b1849 b2296 b2779 b2925 b2097 b0160 b3844 b1747 b3236 b0120 b3962 b1982 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b3946 b0825 b4267 b1033 b0595 b4374 b0675 b2361 b2291 b1415 b1014 b4014 b0261 b2976 b0822 b2799 b0507 b3709 b1907 b2913 b3161 b0112 b3915 b1444 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b3825 b1380 b1912 b2413 b1473 b0494 b4266 b2842   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.286957 (mmol/gDw/h)
  Minimum Production Rate : 0.062550 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.779300
  EX_glc__D_e : 10.000000
  EX_nh4_e : 3.851529
  EX_so4_e : 0.386820
  EX_pi_e : 0.276801
  EX_k_e : 0.056012
  EX_fe3_e : 0.004610
  EX_mg2_e : 0.002489
  EX_ca2_e : 0.001494
  EX_cl_e : 0.001494
  EX_cu2_e : 0.000203
  EX_mn2_e : 0.000198
  EX_zn2_e : 0.000098
  EX_ni2_e : 0.000093

Product: (mmol/gDw/h)
  EX_h2o_e : 42.377564
  EX_co2_e : 27.806010
  EX_h_e : 8.131370
  EX_pyr_e : 5.178754
  EX_acald_e : 0.870894
  EX_met__L_e : 0.314558
  EX_dxylnt_e : 0.062697
  Auxiliary production reaction : 0.062505
  DM_oxam_c : 0.000321
  DM_5drib_c : 0.000193
  DM_4crsol_c : 0.000064

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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