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 : bwco1gdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (82 of 96: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b3399 b1241 b0351 b3831 b4069 b2502 b2744 b1278 b3708 b3614 b0910 b3752 b2297 b2458 b2781 b1759 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b0675 b2361 b0261 b1701 b1805 b0507 b4381 b2406 b0112 b2975 b0114 b3603 b1539 b2492 b0904 b1533 b3918   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.513433 (mmol/gDw/h)
  Minimum Production Rate : 0.238336 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 22.956336
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.293078
  EX_pi_e : 1.210269
  EX_so4_e : 1.082638
  EX_tungs_e : 0.238336
  EX_k_e : 0.100218
  EX_fe2_e : 0.008246
  EX_mg2_e : 0.004454
  EX_ca2_e : 0.002672
  EX_cl_e : 0.002672
  EX_cu2_e : 0.000364
  EX_mn2_e : 0.000355
  EX_zn2_e : 0.000175
  EX_ni2_e : 0.000166
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 48.183918
  EX_co2_e : 23.713278
  EX_h_e : 9.437613
  EX_ac_e : 3.817966
  Auxiliary production reaction : 0.238336
  EX_thym_e : 0.079498
  DM_oxam_c : 0.014009
  DM_5drib_c : 0.000345
  DM_4crsol_c : 0.000114

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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