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 : gua_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (103 of 123: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3942 b1732 b0238 b0125 b4069 b2744 b3708 b3115 b1849 b2296 b2883 b0477 b2797 b3117 b1814 b4471 b2440 b4374 b2361 b2291 b4064 b4464 b0114 b1539 b2492 b0904 b0516   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.786352 (mmol/gDw/h)
  Minimum Production Rate : 0.197316 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.732465
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.491394
  EX_pi_e : 0.758520
  EX_so4_e : 0.198019
  EX_k_e : 0.153490
  EX_fe2_e : 0.012630
  EX_mg2_e : 0.006822
  EX_ca2_e : 0.004093
  EX_cl_e : 0.004093
  EX_cu2_e : 0.000558
  EX_mn2_e : 0.000543
  EX_zn2_e : 0.000268
  EX_ni2_e : 0.000254
  EX_cobalt2_e : 0.000020

Product: (mmol/gDw/h)
  EX_h2o_e : 48.569429
  EX_co2_e : 25.809399
  EX_h_e : 8.681978
  EX_ac_e : 0.457803
  Auxiliary production reaction : 0.197316
  EX_alltn_e : 0.003070
  DM_5drib_c : 0.000177
  DM_4crsol_c : 0.000175

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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