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 : 5caiz_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (66 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b3399 b2744 b3708 b3008 b0871 b3115 b1849 b2296 b2925 b2097 b2926 b0160 b0517 b1982 b2688 b2797 b3117 b1814 b4471 b3449 b3946 b0825 b4374 b0675 b2361 b2291 b0261 b2239 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b1380   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.579178 (mmol/gDw/h)
  Minimum Production Rate : 0.199413 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.130456
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.853313
  EX_pi_e : 0.758092
  EX_so4_e : 0.145849
  EX_k_e : 0.113052
  EX_fe2_e : 0.009302
  EX_mg2_e : 0.005024
  EX_ca2_e : 0.003015
  EX_cl_e : 0.003015
  EX_cu2_e : 0.000411
  EX_mn2_e : 0.000400
  EX_zn2_e : 0.000197
  EX_ni2_e : 0.000187
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 46.150265
  EX_co2_e : 26.675007
  EX_h_e : 8.704832
  EX_pyr_e : 2.585461
  Auxiliary production reaction : 0.199413
  DM_5drib_c : 0.000389
  DM_4crsol_c : 0.000129

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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