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 : gsn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3399 b3942 b1732 b4069 b4384 b2744 b3708 b3008 b3752 b3115 b1849 b2296 b2407 b1982 b2797 b3117 b1814 b4471 b4381 b0114 b2366 b2492 b0904 b1533 b3927 b3821 b0516 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.751874 (mmol/gDw/h)
  Minimum Production Rate : 0.316510 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.426529
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.714472
  EX_pi_e : 0.725263
  EX_so4_e : 0.189337
  EX_k_e : 0.146761
  EX_fe2_e : 0.012076
  EX_mg2_e : 0.006523
  EX_ca2_e : 0.003914
  EX_cl_e : 0.003914
  EX_cu2_e : 0.000533
  EX_mn2_e : 0.000520
  EX_zn2_e : 0.000256
  EX_ni2_e : 0.000243
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.429958
  EX_co2_e : 25.072875
  EX_h_e : 8.940545
  EX_ac_e : 0.437731
  Auxiliary production reaction : 0.316510
  EX_alltn_e : 0.002935
  DM_mththf_c : 0.002431
  DM_5drib_c : 0.000505
  DM_4crsol_c : 0.000168

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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