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 (101 of 123: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b4069 b2744 b3708 b3115 b1849 b2296 b2926 b3236 b2883 b2797 b3117 b1814 b4471 b2210 b2440 b0411 b4381 b0511 b0114 b1539 b2492 b0904 b1533 b0515 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.683663 (mmol/gDw/h)
  Minimum Production Rate : 0.290005 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.101340
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.835362
  EX_pi_e : 0.659465
  EX_so4_e : 0.172160
  EX_k_e : 0.133446
  EX_fe2_e : 0.010980
  EX_mg2_e : 0.005931
  EX_cl_e : 0.003558
  EX_ca2_e : 0.003558
  EX_cu2_e : 0.000485
  EX_mn2_e : 0.000472
  EX_zn2_e : 0.000233
  EX_ni2_e : 0.000221
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 50.646724
  EX_co2_e : 29.688896
  EX_h_e : 8.131648
  EX_ac_e : 0.398019
  Auxiliary production reaction : 0.290005
  EX_xan_e : 0.000460
  DM_mththf_c : 0.000306
  DM_5drib_c : 0.000154
  DM_4crsol_c : 0.000152

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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