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 : adp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 89: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b3553 b3399 b4069 b2744 b3926 b2297 b2458 b2925 b2097 b0160 b1238 b1004 b3713 b1109 b0046 b3236 b1638 b1982 b4139 b3946 b0825 b1033 b0675 b2361 b0261 b1602 b4381 b0114 b0529 b2492 b0904 b3029 b1380 b2660 b1771 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.393951 (mmol/gDw/h)
  Minimum Production Rate : 0.181806 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 31.848610
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.163671
  EX_pi_e : 0.743619
  EX_so4_e : 0.099205
  EX_k_e : 0.076897
  EX_fe2_e : 0.006327
  EX_mg2_e : 0.003418
  EX_ca2_e : 0.002051
  EX_cl_e : 0.002051
  EX_cu2_e : 0.000279
  EX_mn2_e : 0.000272
  EX_zn2_e : 0.000134
  EX_ni2_e : 0.000127

Product: (mmol/gDw/h)
  EX_h2o_e : 45.001528
  EX_co2_e : 32.234884
  EX_h_e : 9.235147
  EX_ac_e : 4.888140
  Auxiliary production reaction : 0.181806
  DM_5drib_c : 0.000264
  DM_4crsol_c : 0.000088

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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