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 : dnad_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (31 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3399 b4382 b1241 b0351 b4069 b4384 b2744 b2297 b2458 b2926 b2407 b1851 b1982 b3616 b3589 b3665 b0675 b2361 b0261 b0507 b0112 b0114 b0529 b2492 b0904 b1380 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.437851 (mmol/gDw/h)
  Minimum Production Rate : 0.430834 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.069107
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.949388
  EX_pi_e : 1.284022
  EX_so4_e : 0.110260
  EX_k_e : 0.085465
  EX_fe2_e : 0.007032
  EX_mg2_e : 0.003798
  EX_ca2_e : 0.002279
  EX_cl_e : 0.002279
  EX_cu2_e : 0.000310
  EX_mn2_e : 0.000303
  EX_zn2_e : 0.000149
  EX_ni2_e : 0.000141
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 49.385122
  EX_co2_e : 24.301564
  EX_h_e : 7.637026
  EX_thymd_e : 0.816590
  Auxiliary production reaction : 0.430834
  EX_ac_e : 0.254911
  EX_ade_e : 0.000490
  DM_5drib_c : 0.000294
  DM_4crsol_c : 0.000098

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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