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 : gdpddman_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4467 b2836 b3399 b4069 b2744 b3708 b2297 b2458 b2926 b0160 b1238 b1004 b3713 b1109 b0046 b3236 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b1602 b4381 b1727 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b1380 b2660 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.452361 (mmol/gDw/h)
  Minimum Production Rate : 0.191619 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.448463
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.843549
  EX_pi_e : 0.819587
  EX_so4_e : 0.113913
  EX_k_e : 0.088298
  EX_fe2_e : 0.007265
  EX_mg2_e : 0.003924
  EX_ca2_e : 0.002355
  EX_cl_e : 0.002355
  EX_cu2_e : 0.000321
  EX_mn2_e : 0.000313
  EX_zn2_e : 0.000154
  EX_ni2_e : 0.000146
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.658926
  EX_co2_e : 37.839054
  EX_h_e : 4.994683
  EX_ac_e : 0.263358
  Auxiliary production reaction : 0.191619
  DM_5drib_c : 0.000304
  DM_4crsol_c : 0.000101

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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