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 : paps_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (21 of 36: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b2836 b3399 b4382 b1241 b0351 b4069 b2744 b3708 b3115 b1849 b2296 b0160 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b0675 b2361 b0261 b4381 b2406 b0112 b0114 b1539 b2492 b0904 b1533   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.590573 (mmol/gDw/h)
  Minimum Production Rate : 0.868157 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.499233
  EX_nh4_e : 10.718926
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.305984
  EX_so4_e : 1.016875
  EX_k_e : 0.115276
  EX_fe2_e : 0.009485
  EX_mg2_e : 0.005123
  EX_ca2_e : 0.003074
  EX_cl_e : 0.003074
  EX_cu2_e : 0.000419
  EX_mn2_e : 0.000408
  EX_zn2_e : 0.000201
  EX_ni2_e : 0.000191
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 50.338873
  EX_co2_e : 22.589268
  EX_h_e : 10.274656
  EX_ac_e : 2.243762
  Auxiliary production reaction : 0.868157
  DM_5drib_c : 0.000396
  DM_4crsol_c : 0.000132

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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