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 : prpncoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (49 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b3399 b4382 b1241 b0351 b4069 b2502 b2744 b3708 b2297 b2458 b3617 b3124 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b4381 b2406 b0112 b2789 b3127 b2975 b0114 b3603 b2366 b2492 b0904 b1533 b3821 b0514   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.509080 (mmol/gDw/h)
  Minimum Production Rate : 0.498906 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 20.171694
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.004251
  EX_pi_e : 1.987780
  EX_so4_e : 0.627103
  EX_k_e : 0.099369
  EX_fe2_e : 0.008176
  EX_mg2_e : 0.004416
  EX_ca2_e : 0.002650
  EX_cl_e : 0.002650
  EX_cu2_e : 0.000361
  EX_mn2_e : 0.000352
  EX_zn2_e : 0.000174
  EX_ni2_e : 0.000164
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 45.684463
  EX_co2_e : 21.736265
  EX_h_e : 8.884970
  EX_ac_e : 2.682844
  Auxiliary production reaction : 0.498906
  DM_oxam_c : 0.013890
  DM_5drib_c : 0.000342
  DM_4crsol_c : 0.000114

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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