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 : 5pg35pg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (72 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3708 b3008 b3752 b0871 b2407 b1238 b3236 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b0261 b4381 b2406 b0114 b1539 b2492 b0904 b1533 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.619503 (mmol/gDw/h)
  Minimum Production Rate : 0.373280 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.938291
  EX_o2_e : 273.488619
  EX_nh4_e : 10.423378
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.344136
  EX_so4_e : 0.156003
  EX_k_e : 0.120923
  EX_mg2_e : 0.005374
  EX_ca2_e : 0.003225
  EX_cl_e : 0.003225
  EX_cu2_e : 0.000439
  EX_mn2_e : 0.000428
  EX_zn2_e : 0.000211
  EX_ni2_e : 0.000200
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990050
  EX_h2o_e : 549.166313
  EX_co2_e : 23.479931
  EX_acald_e : 1.812674
  Auxiliary production reaction : 0.373280
  DM_5drib_c : 0.000416
  DM_4crsol_c : 0.000138

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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