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 : seramp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b3708 b2297 b2458 b3617 b2883 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0261 b0411 b4381 b0114 b1539 b2492 b0904 b1533   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.610605 (mmol/gDw/h)
  Minimum Production Rate : 0.609054 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 22.293614
  EX_nh4_e : 10.248802
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.198047
  EX_so4_e : 0.153762
  EX_k_e : 0.119186
  EX_fe2_e : 0.009807
  EX_mg2_e : 0.005297
  EX_ca2_e : 0.003178
  EX_cl_e : 0.003178
  EX_cu2_e : 0.000433
  EX_mn2_e : 0.000422
  EX_zn2_e : 0.000208
  EX_ni2_e : 0.000197
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 46.420767
  EX_co2_e : 21.769632
  EX_h_e : 10.671089
  EX_ac_e : 2.624394
  Auxiliary production reaction : 0.609054
  DM_5drib_c : 0.000410
  DM_4crsol_c : 0.000136

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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