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 : gdpmann_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (100 of 108: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 52
  Gene deletion: b3553 b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b1479 b3752 b0871 b2779 b3844 b3236 b2883 b2463 b3962 b1982 b0104 b3616 b3589 b2210 b4267 b1033 b1415 b3551 b1014 b3945 b2913 b4219 b1832 b1778 b4381 b0112 b2868 b4064 b4464 b0114 b0529 b2492 b0904 b1380 b0325 b1710 b2480 b1511 b4266 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.347839 (mmol/gDw/h)
  Minimum Production Rate : 0.413118 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 34.845856
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.585823
  EX_pi_e : 1.188833
  EX_so4_e : 0.087593
  EX_k_e : 0.067896
  EX_fe3_e : 0.005587
  EX_mg2_e : 0.003018
  EX_ca2_e : 0.001811
  EX_cl_e : 0.001811
  EX_cu2_e : 0.000247
  EX_mn2_e : 0.000240
  EX_zn2_e : 0.000119
  EX_ni2_e : 0.000112

Product: (mmol/gDw/h)
  EX_h2o_e : 51.356573
  EX_co2_e : 34.669955
  EX_h_e : 5.177789
  EX_acald_e : 1.416889
  Auxiliary production reaction : 0.426653
  EX_adn_e : 0.138951
  EX_ade_e : 0.000234
  EX_dxylnt_e : 0.000233
  EX_mththf_e : 0.000156
  DM_5drib_c : 0.000078
  DM_4crsol_c : 0.000078

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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