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 : adphep_DD_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (66 of 99: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b2836 b3399 b3831 b4069 b2744 b3708 b3008 b2297 b2458 b0160 b3844 b1779 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b4381 b2406 b0114 b1539 b2492 b0904 b2578 b1533 b3927 b0594 b3447 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.467851 (mmol/gDw/h)
  Minimum Production Rate : 0.185904 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.556977
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.982260
  EX_pi_e : 0.823094
  EX_so4_e : 0.117815
  EX_k_e : 0.091321
  EX_fe2_e : 0.007516
  EX_mg2_e : 0.004059
  EX_ca2_e : 0.002435
  EX_cl_e : 0.002435
  EX_cu2_e : 0.000332
  EX_mn2_e : 0.000323
  EX_zn2_e : 0.000160
  EX_ni2_e : 0.000151
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.048010
  EX_co2_e : 37.090736
  EX_h_e : 5.128886
  EX_ac_e : 0.272378
  Auxiliary production reaction : 0.185901
  DM_5drib_c : 0.000314
  DM_4crsol_c : 0.000104

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
Contact