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 : fprica_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (60 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3399 b4069 b2502 b2744 b3708 b2297 b2458 b2926 b1238 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b4381 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b3821 b0516 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.480614 (mmol/gDw/h)
  Minimum Production Rate : 0.202320 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.159646
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.007372
  EX_pi_e : 0.665923
  EX_so4_e : 0.121028
  EX_k_e : 0.093812
  EX_fe2_e : 0.007719
  EX_mg2_e : 0.004169
  EX_ca2_e : 0.002502
  EX_cl_e : 0.002502
  EX_cu2_e : 0.000341
  EX_mn2_e : 0.000332
  EX_zn2_e : 0.000164
  EX_ni2_e : 0.000155
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.401869
  EX_co2_e : 37.673857
  EX_h_e : 5.512662
  EX_ac_e : 0.279807
  Auxiliary production reaction : 0.202320
  EX_alltn_e : 0.001876
  DM_mththf_c : 0.001768
  DM_5drib_c : 0.000108
  DM_4crsol_c : 0.000107

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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