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 : 12ppd__S_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 92: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b4467 b0474 b2518 b1241 b0351 b4069 b2930 b4232 b3697 b3925 b3115 b1849 b2296 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b2690 b2210 b3945 b1602 b2913 b1727 b0529 b2492 b0904 b1380 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.397989 (mmol/gDw/h)
  Minimum Production Rate : 0.278764 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.244764
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.298250
  EX_pi_e : 0.383903
  EX_so4_e : 0.100222
  EX_k_e : 0.077685
  EX_fe2_e : 0.006392
  EX_mg2_e : 0.003453
  EX_ca2_e : 0.002072
  EX_cl_e : 0.002072
  EX_cu2_e : 0.000282
  EX_mn2_e : 0.000275
  EX_zn2_e : 0.000136
  EX_ni2_e : 0.000129

Product: (mmol/gDw/h)
  EX_h2o_e : 42.603877
  EX_co2_e : 33.346864
  EX_h_e : 7.423473
  EX_ac_e : 3.766588
  EX_etoh_e : 0.974019
  EX_12ppd__S_e : 0.278764
  DM_5drib_c : 0.000090
  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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