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 : dadp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (77 of 95: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3553 b3399 b4069 b2744 b3115 b1849 b2296 b2925 b2097 b2926 b1004 b3713 b1109 b0046 b3236 b2690 b1033 b0261 b1602 b2913 b4381 b1727 b0114 b0529 b2492 b0904 b1380 b1771 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.397768 (mmol/gDw/h)
  Minimum Production Rate : 0.130002 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.544471
  EX_o2_e : 291.293141
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.988578
  EX_pi_e : 0.643694
  EX_so4_e : 0.100166
  EX_k_e : 0.077642
  EX_mg2_e : 0.003451
  EX_ca2_e : 0.002070
  EX_cl_e : 0.002070
  EX_cu2_e : 0.000282
  EX_mn2_e : 0.000275
  EX_zn2_e : 0.000136
  EX_ni2_e : 0.000128

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993611
  EX_h2o_e : 554.143766
  EX_co2_e : 41.856890
  EX_ac_e : 0.231575
  Auxiliary production reaction : 0.130002
  EX_hxan_e : 0.010676
  DM_5drib_c : 0.000089
  DM_4crsol_c : 0.000089

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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