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 : btn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (7 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b2836 b4384 b3708 b3008 b0871 b0030 b2407 b2920 b1982 b2797 b3117 b1814 b4471 b0261 b4381 b2406 b0114 b0728 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.751268 (mmol/gDw/h)
  Minimum Production Rate : 0.068823 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.218869
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.595388
  EX_pi_e : 0.724678
  EX_so4_e : 0.326829
  EX_k_e : 0.146642
  EX_fe2_e : 0.012066
  EX_mg2_e : 0.006517
  EX_ca2_e : 0.003910
  EX_cl_e : 0.003910
  EX_cu2_e : 0.000533
  EX_mn2_e : 0.000519
  EX_zn2_e : 0.000256
  EX_ni2_e : 0.000243
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.175265
  EX_co2_e : 27.028726
  EX_h_e : 7.178240
  DM_5drib_c : 0.069327
  EX_meoh_e : 0.068824
  DM_amob_c : 0.068824
  Auxiliary production reaction : 0.068823
  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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