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 (58 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3399 b4384 b2744 b3708 b3008 b0871 b2925 b2097 b2926 b2690 b1982 b2797 b3117 b1814 b4471 b2440 b1623 b3945 b4381 b0511 b0114 b2366 b2492 b0904 b1533 b0515 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.380476 (mmol/gDw/h)
  Minimum Production Rate : 0.077632 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.934952
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.149953
  EX_pi_e : 0.522273
  EX_so4_e : 0.095811
  EX_k_e : 0.074266
  EX_fe2_e : 0.006111
  EX_mg2_e : 0.003301
  EX_cl_e : 0.001980
  EX_ca2_e : 0.001980
  EX_cu2_e : 0.000270
  EX_mn2_e : 0.000263
  EX_zn2_e : 0.000130
  EX_ni2_e : 0.000123

Product: (mmol/gDw/h)
  EX_h2o_e : 44.028923
  EX_co2_e : 28.784924
  EX_h_e : 8.253431
  EX_pyr_e : 4.794252
  Auxiliary production reaction : 0.077632
  EX_xan_e : 0.010212
  DM_5drib_c : 0.000086
  DM_4crsol_c : 0.000085

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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