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 : 2h3oppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b1241 b0351 b4069 b4384 b2744 b2930 b4232 b3697 b3925 b2297 b2458 b2779 b3617 b0030 b2407 b2690 b1982 b4374 b2361 b2291 b0261 b0411 b3945 b0112 b0114 b0529 b2492 b0904 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.334750 (mmol/gDw/h)
  Minimum Production Rate : 0.320882 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.636790
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.257191
  EX_pi_e : 0.322902
  EX_so4_e : 0.084297
  EX_k_e : 0.065341
  EX_fe2_e : 0.005376
  EX_mg2_e : 0.002904
  EX_ca2_e : 0.001742
  EX_cl_e : 0.001742
  EX_cu2_e : 0.000237
  EX_mn2_e : 0.000231
  EX_zn2_e : 0.000114
  EX_ni2_e : 0.000108

Product: (mmol/gDw/h)
  EX_h2o_e : 42.719721
  EX_co2_e : 30.350555
  EX_h_e : 7.662418
  EX_ac_e : 2.981885
  DM_oxam_c : 0.641915
  DM_5drib_c : 0.641765
  DM_4crsol_c : 0.641615
  Auxiliary production reaction : 0.320882

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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