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 : eig3p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (46 of 89: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b3115 b1849 b2296 b2779 b2926 b2883 b3616 b3589 b1623 b3665 b0411 b4381 b0112 b3654 b3714 b3664 b0114 b0529 b2492 b0904 b0516 b3662 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.491721 (mmol/gDw/h)
  Minimum Production Rate : 1.860330 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.518174
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.082676
  EX_pi_e : 2.334648
  EX_so4_e : 0.123825
  EX_k_e : 0.095981
  EX_fe2_e : 0.007898
  EX_mg2_e : 0.004266
  EX_ca2_e : 0.002559
  EX_cl_e : 0.002559
  EX_cu2_e : 0.000349
  EX_mn2_e : 0.000340
  EX_zn2_e : 0.000168
  EX_ni2_e : 0.000159
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 47.975473
  EX_co2_e : 25.598753
  EX_h_e : 9.792155
  Auxiliary production reaction : 1.860330
  EX_ac_e : 1.501896
  EX_alltn_e : 0.012866
  DM_mththf_c : 0.000220
  DM_5drib_c : 0.000111
  DM_4crsol_c : 0.000110

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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