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 : forcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b3831 b4069 b4384 b3708 b3008 b3752 b2930 b4232 b3697 b3925 b2297 b2458 b2407 b1779 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b0261 b1701 b1805 b0507 b4381 b2406 b0112 b2975 b0114 b3603 b2366 b2492 b0904 b0591 b2578 b1533 b3927 b1380 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.572417 (mmol/gDw/h)
  Minimum Production Rate : 0.145485 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.434551
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.201087
  EX_pi_e : 0.988611
  EX_so4_e : 0.289631
  EX_k_e : 0.111732
  EX_fe2_e : 0.009194
  EX_mg2_e : 0.004966
  EX_cl_e : 0.002979
  EX_ca2_e : 0.002979
  EX_cu2_e : 0.000406
  EX_mn2_e : 0.000396
  EX_zn2_e : 0.000195
  EX_ni2_e : 0.000185
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 46.754931
  EX_co2_e : 28.728009
  EX_h_e : 7.984173
  EX_ac_e : 2.286843
  Auxiliary production reaction : 0.145485
  DM_oxam_c : 0.000641
  DM_5drib_c : 0.000384
  DM_4crsol_c : 0.000128

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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