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 : aps_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (38 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3399 b4382 b1241 b0351 b4069 b2502 b4384 b2744 b3115 b1849 b2296 b3617 b2407 b0675 b2361 b0112 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b0529 b2492 b0904 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.572106 (mmol/gDw/h)
  Minimum Production Rate : 1.097195 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.199960
  EX_nh4_e : 11.664678
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.649053
  EX_so4_e : 1.241263
  EX_k_e : 0.111671
  EX_fe2_e : 0.009189
  EX_mg2_e : 0.004963
  EX_ca2_e : 0.002978
  EX_cl_e : 0.002978
  EX_cu2_e : 0.000406
  EX_mn2_e : 0.000395
  EX_zn2_e : 0.000195
  EX_ni2_e : 0.000185
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 51.049147
  EX_co2_e : 21.677858
  EX_h_e : 10.481611
  EX_ac_e : 1.933283
  Auxiliary production reaction : 1.097195
  DM_mththf_c : 0.000256
  DM_5drib_c : 0.000129
  DM_4crsol_c : 0.000128

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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