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 : acetol_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (52 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4467 b1478 b1241 b0351 b2930 b4232 b3697 b3925 b3115 b1849 b2296 b2779 b1004 b3713 b1109 b0046 b3236 b2690 b1525 b2210 b4015 b2661 b3945 b1602 b1380 b2660 b0606 b0221 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.538203 (mmol/gDw/h)
  Minimum Production Rate : 1.526140 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.790376
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.812548
  EX_pi_e : 0.519154
  EX_so4_e : 0.135530
  EX_k_e : 0.105053
  EX_fe3_e : 0.008644
  EX_mg2_e : 0.004669
  EX_ca2_e : 0.002801
  EX_cl_e : 0.002801
  EX_cu2_e : 0.000382
  EX_mn2_e : 0.000372
  EX_zn2_e : 0.000184
  EX_ni2_e : 0.000174
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 46.912279
  EX_co2_e : 32.704144
  EX_h_e : 5.267204
  Auxiliary production reaction : 1.526140
  EX_ac_e : 0.313334
  DM_5drib_c : 0.000121
  DM_4crsol_c : 0.000120

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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