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 (85 of 95: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b1241 b0351 b4069 b3708 b2297 b2458 b2925 b2097 b2926 b0030 b2407 b2690 b3962 b4139 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b0675 b0822 b4381 b2406 b2868 b1727 b0114 b2366 b2492 b0904 b0325 b0508 b4266 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.397567 (mmol/gDw/h)
  Minimum Production Rate : 0.389799 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.056001
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.285367
  EX_pi_e : 1.163094
  EX_so4_e : 0.100115
  EX_k_e : 0.077602
  EX_fe2_e : 0.006385
  EX_mg2_e : 0.003449
  EX_ca2_e : 0.002069
  EX_cl_e : 0.002069
  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_h2o_e : 52.760210
  EX_co2_e : 37.098142
  EX_h_e : 6.570546
  EX_ac_e : 1.315663
  Auxiliary production reaction : 0.389799
  EX_hxan_e : 0.010670
  EX_mththf_e : 0.000178
  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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