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 : nadph_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (58 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4467 b1478 b1241 b4069 b4384 b3752 b3115 b1849 b2296 b2407 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b0261 b0411 b2799 b3945 b1602 b2342 b3845 b2913 b4381 b3915 b2975 b3603 b0529 b2492 b0904 b1380 b0606 b2285 b1007 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.320240 (mmol/gDw/h)
  Minimum Production Rate : 0.526962 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.772533
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.149091
  EX_pi_e : 1.889790
  EX_so4_e : 0.080643
  EX_k_e : 0.062509
  EX_fe3_e : 0.005143
  EX_mg2_e : 0.002778
  EX_ca2_e : 0.001667
  EX_cl_e : 0.001667
  EX_cu2_e : 0.000227
  EX_mn2_e : 0.000221
  EX_zn2_e : 0.000109
  EX_ni2_e : 0.000103

Product: (mmol/gDw/h)
  EX_h2o_e : 52.662856
  EX_co2_e : 33.138990
  EX_h_e : 6.908197
  EX_ac_e : 1.323958
  Auxiliary production reaction : 0.526962
  EX_ade_e : 0.000358
  DM_5drib_c : 0.000215
  DM_4crsol_c : 0.000071

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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