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 : dpcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b3399 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2502 b2744 b3708 b3008 b0871 b3617 b2797 b3117 b1814 b4471 b1623 b3665 b0675 b2361 b4381 b2406 b0112 b3654 b3714 b3664 b0114 b2366 b2492 b0904 b1533 b3825 b4141 b1798 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.602774 (mmol/gDw/h)
  Minimum Production Rate : 0.355719 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.735752
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.999939
  EX_pi_e : 1.292877
  EX_so4_e : 0.507510
  EX_k_e : 0.117657
  EX_fe2_e : 0.009681
  EX_mg2_e : 0.005229
  EX_ca2_e : 0.003137
  EX_cl_e : 0.003137
  EX_cu2_e : 0.000427
  EX_mn2_e : 0.000417
  EX_zn2_e : 0.000206
  EX_ni2_e : 0.000195
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 46.580266
  EX_co2_e : 24.259733
  EX_h_e : 6.605683
  EX_acald_e : 1.763861
  Auxiliary production reaction : 0.355719
  DM_mththf_c : 0.000270
  DM_5drib_c : 0.000136
  DM_4crsol_c : 0.000134

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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