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 : gdpofuc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (66 of 71: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 51
  Gene deletion: b3942 b1732 b3846 b1241 b0351 b4069 b4384 b2744 b1479 b3752 b2297 b2458 b2779 b2407 b3844 b3236 b0907 b2463 b3962 b1982 b0104 b3616 b3589 b2210 b4267 b0675 b1415 b3551 b1014 b0822 b4219 b1832 b1778 b4381 b0112 b2868 b0114 b0509 b3125 b0529 b2492 b0904 b1380 b0325 b1710 b2480 b4042 b1511 b4266 b3662 b1813   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.333556 (mmol/gDw/h)
  Minimum Production Rate : 0.537729 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.156535
  EX_o2_e : 284.540198
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.800877
  EX_pi_e : 1.397209
  EX_so4_e : 0.083996
  EX_k_e : 0.065108
  EX_mg2_e : 0.002894
  EX_ca2_e : 0.001736
  EX_cl_e : 0.001736
  EX_cu2_e : 0.000236
  EX_mn2_e : 0.000230
  EX_zn2_e : 0.000114
  EX_ni2_e : 0.000108

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994643
  EX_h2o_e : 551.378173
  EX_co2_e : 33.385165
  EX_ac_e : 1.650072
  Auxiliary production reaction : 0.537729
  EX_adn_e : 0.101746
  EX_ade_e : 0.000224
  EX_mththf_e : 0.000149
  EX_dxylnt_e : 0.000149
  DM_5drib_c : 0.000075
  DM_4crsol_c : 0.000074

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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