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 : cdpdodec11eg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b1054 b2836 b3831 b3614 b0910 b3752 b4152 b2781 b3844 b1612 b1611 b4122 b1759 b4138 b4123 b0621 b4381 b2406 b3915 b2197 b3918 b0789 b1249 b1695 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.539333 (mmol/gDw/h)
  Minimum Production Rate : 0.284052 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 16.871365
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.873734
  EX_pi_e : 1.088347
  EX_so4_e : 0.135815
  EX_k_e : 0.105274
  EX_fe3_e : 0.008662
  EX_mg2_e : 0.004679
  EX_ca2_e : 0.002807
  EX_cl_e : 0.002807
  EX_cu2_e : 0.000382
  EX_mn2_e : 0.000373
  EX_zn2_e : 0.000184
  EX_ni2_e : 0.000174
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 40.560664
  EX_co2_e : 21.575549
  EX_h_e : 6.571562
  EX_succ_e : 0.562412
  Auxiliary production reaction : 0.284052
  EX_ura_e : 0.098415
  EX_hxa_e : 0.001589
  DM_5drib_c : 0.000121
  DM_4crsol_c : 0.000120

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