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 : dump_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (49 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b3553 b1478 b1241 b4069 b4384 b3752 b2297 b2458 b2779 b3844 b1004 b3713 b1109 b0046 b3236 b0937 b1982 b1033 b0261 b0411 b2799 b3945 b1602 b2913 b4381 b4064 b4464 b0509 b3125 b0529 b2492 b0904 b1380 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.364896 (mmol/gDw/h)
  Minimum Production Rate : 1.147797 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.349614
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.238483
  EX_pi_e : 1.499778
  EX_so4_e : 0.091888
  EX_k_e : 0.071225
  EX_fe2_e : 0.005861
  EX_mg2_e : 0.003165
  EX_ca2_e : 0.001899
  EX_cl_e : 0.001899
  EX_cu2_e : 0.000259
  EX_mn2_e : 0.000252
  EX_zn2_e : 0.000124
  EX_ni2_e : 0.000118

Product: (mmol/gDw/h)
  EX_h2o_e : 50.654135
  EX_co2_e : 32.979574
  EX_h_e : 6.505490
  Auxiliary production reaction : 1.147797
  EX_ac_e : 0.855043
  EX_ade_e : 0.000408
  DM_5drib_c : 0.000245
  DM_4crsol_c : 0.000081

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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