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 : glyclt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (24 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b1241 b0351 b4069 b4384 b3752 b2297 b2458 b2779 b2926 b3617 b2407 b1982 b0261 b4388 b4381 b2406 b0112 b2789 b3127 b2975 b0114 b3603 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.421307 (mmol/gDw/h)
  Minimum Production Rate : 0.807706 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.719763
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.357977
  EX_pi_e : 0.406395
  EX_so4_e : 0.106094
  EX_k_e : 0.082236
  EX_fe2_e : 0.006767
  EX_mg2_e : 0.003655
  EX_ca2_e : 0.002193
  EX_cl_e : 0.002193
  EX_cu2_e : 0.000299
  EX_mn2_e : 0.000291
  EX_zn2_e : 0.000144
  EX_ni2_e : 0.000136
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 40.781708
  EX_co2_e : 25.618087
  EX_h_e : 8.378614
  EX_ac_e : 2.083979
  DM_oxam_c : 0.807895
  DM_5drib_c : 0.807707
  Auxiliary production reaction : 0.807706
  DM_4crsol_c : 0.807518

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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