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 : didp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b3553 b1241 b0351 b4069 b2744 b3708 b2297 b2458 b2779 b3236 b2883 b3962 b2797 b3117 b1814 b4471 b3616 b3589 b2210 b4267 b1033 b0675 b0261 b0822 b2799 b4381 b2406 b2868 b4064 b4464 b0114 b2366 b2492 b0904 b1533 b4266   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.433021 (mmol/gDw/h)
  Minimum Production Rate : 0.424496 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 35.011512
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.432687
  EX_pi_e : 1.266688
  EX_so4_e : 0.109043
  EX_k_e : 0.084523
  EX_fe2_e : 0.006955
  EX_mg2_e : 0.003756
  EX_ca2_e : 0.002254
  EX_cl_e : 0.002254
  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_h2o_e : 51.702609
  EX_co2_e : 35.057540
  EX_h_e : 6.743297
  EX_ac_e : 1.432927
  Auxiliary production reaction : 0.424496
  EX_ade_e : 0.011622
  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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