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 : glx_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b1241 b0351 b4069 b4384 b2744 b3752 b3115 b1849 b2296 b3617 b2407 b3124 b1982 b4374 b2361 b2291 b0261 b0411 b0112 b0114 b0529 b2492 b0904 b0514 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.493317 (mmol/gDw/h)
  Minimum Production Rate : 0.945760 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 20.709020
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.273766
  EX_pi_e : 0.475857
  EX_so4_e : 0.124227
  EX_k_e : 0.096292
  EX_fe2_e : 0.007923
  EX_mg2_e : 0.004280
  EX_ca2_e : 0.002568
  EX_cl_e : 0.002568
  EX_cu2_e : 0.000350
  EX_mn2_e : 0.000341
  EX_zn2_e : 0.000168
  EX_ni2_e : 0.000159
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 39.989162
  EX_co2_e : 21.288006
  EX_h_e : 9.037443
  EX_ac_e : 1.666925
  DM_oxam_c : 0.945982
  DM_5drib_c : 0.945761
  Auxiliary production reaction : 0.945760
  DM_4crsol_c : 0.945540

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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