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 : frdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b1241 b0351 b4069 b2502 b2744 b3115 b1849 b2296 b2779 b1982 b3616 b3589 b4374 b0675 b2361 b0261 b4388 b4381 b0112 b0511 b0114 b0529 b2492 b0904 b0516   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.488907 (mmol/gDw/h)
  Minimum Production Rate : 0.616123 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 22.934490
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.333510
  EX_pi_e : 1.703848
  EX_so4_e : 0.123116
  EX_k_e : 0.095431
  EX_fe2_e : 0.007852
  EX_mg2_e : 0.004241
  EX_ca2_e : 0.002545
  EX_cl_e : 0.002545
  EX_cu2_e : 0.000347
  EX_mn2_e : 0.000338
  EX_zn2_e : 0.000167
  EX_ni2_e : 0.000158
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 43.129874
  EX_co2_e : 27.634652
  EX_h_e : 5.423679
  EX_ac_e : 1.494173
  Auxiliary production reaction : 0.616123
  EX_xan_e : 0.013340
  DM_5drib_c : 0.000328
  DM_4crsol_c : 0.000109

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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