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 : 5aizc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b2836 b3399 b1241 b0351 b4069 b2502 b4384 b2744 b3708 b3752 b3115 b1849 b2296 b3236 b2883 b1779 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b1623 b4374 b2361 b2291 b0261 b0411 b0112 b0114 b0509 b3125 b1539 b2492 b0904 b1533 b0508 b0516 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.457212 (mmol/gDw/h)
  Minimum Production Rate : 1.365569 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.835919
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.041697
  EX_pi_e : 1.806598
  EX_so4_e : 0.115135
  EX_k_e : 0.089245
  EX_fe2_e : 0.007343
  EX_mg2_e : 0.003966
  EX_ca2_e : 0.002380
  EX_cl_e : 0.002380
  EX_cu2_e : 0.000324
  EX_mn2_e : 0.000316
  EX_zn2_e : 0.000156
  EX_ni2_e : 0.000148
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 47.091555
  EX_co2_e : 24.076986
  EX_h_e : 12.091963
  EX_ac_e : 2.419923
  Auxiliary production reaction : 1.365569
  EX_alltn_e : 0.001785
  DM_5drib_c : 0.001580
  EX_glyclt_e : 0.001579
  DM_4crsol_c : 0.001375

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.

Last updated: 21-Sep-2023
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