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 : imacp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (45 of 103: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b2836 b3399 b1241 b0351 b4069 b2744 b3708 b3115 b1849 b2296 b3617 b1238 b2883 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b0411 b4381 b2406 b0112 b0114 b1539 b2492 b0904 b1533 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.583373 (mmol/gDw/h)
  Minimum Production Rate : 1.745673 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 989.795456
  EX_o2_e : 272.518194
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.791720
  EX_pi_e : 2.308397
  EX_so4_e : 0.146905
  EX_k_e : 0.113870
  EX_mg2_e : 0.005061
  EX_ca2_e : 0.003036
  EX_cl_e : 0.003036
  EX_cu2_e : 0.000414
  EX_mn2_e : 0.000403
  EX_zn2_e : 0.000199
  EX_ni2_e : 0.000188
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990630
  EX_h2o_e : 548.767369
  EX_co2_e : 22.892760
  Auxiliary production reaction : 1.745673
  EX_ac_e : 1.343568
  DM_5drib_c : 0.000391
  DM_4crsol_c : 0.000130

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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