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 (6 of 92: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4467 b1241 b0351 b0871 b2925 b2097 b3844 b1004 b3713 b1109 b0046 b3236 b2690 b4015 b3945 b1602 b2913 b4381 b1727 b0755 b3612 b2492 b0904 b1380 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.433292 (mmol/gDw/h)
  Minimum Production Rate : 2.144613 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 996.011780
  EX_o2_e : 282.710501
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.679518
  EX_pi_e : 0.417956
  EX_so4_e : 0.109112
  EX_k_e : 0.084576
  EX_mg2_e : 0.003759
  EX_ca2_e : 0.002255
  EX_cl_e : 0.002255
  EX_cu2_e : 0.000307
  EX_mn2_e : 0.000299
  EX_zn2_e : 0.000148
  EX_ni2_e : 0.000140
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993041
  EX_h2o_e : 545.075463
  EX_co2_e : 35.781509
  EX_12ppd__S_e : 2.144613
  DM_5drib_c : 0.000097
  DM_4crsol_c : 0.000097

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.

Last updated: 21-Sep-2023
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