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 : gmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (53 of 102: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b0474 b2518 b1241 b0351 b4069 b2502 b2744 b0512 b3115 b1849 b2296 b2926 b3617 b1982 b4374 b0675 b2361 b2291 b0114 b0529 b2492 b0904 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.380448 (mmol/gDw/h)
  Minimum Production Rate : 0.728144 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.895657
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.755465
  EX_pi_e : 1.095126
  EX_so4_e : 0.095804
  EX_k_e : 0.074261
  EX_fe2_e : 0.006110
  EX_mg2_e : 0.003300
  EX_ca2_e : 0.001980
  EX_cl_e : 0.001980
  EX_cu2_e : 0.000270
  EX_mn2_e : 0.000263
  EX_zn2_e : 0.000130
  EX_ni2_e : 0.000123

Product: (mmol/gDw/h)
  EX_h2o_e : 53.313438
  EX_co2_e : 34.518738
  EX_h_e : 8.427991
  EX_ac_e : 1.285623
  Auxiliary production reaction : 0.728144
  EX_alltn_e : 0.001485
  DM_mththf_c : 0.001230
  DM_5drib_c : 0.000255
  DM_4crsol_c : 0.000085

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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