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 : glyc__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4382 b4069 b4384 b3708 b3008 b3115 b1849 b2296 b2779 b0030 b2407 b3844 b1779 b1982 b2797 b3117 b1814 b4471 b0595 b0261 b2406 b0112 b2789 b3127 b0452 b0114 b1539 b2492 b0904 b2578 b1533 b3927 b3825 b3447 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.633570 (mmol/gDw/h)
  Minimum Production Rate : 0.134164 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.677050
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.111535
  EX_pi_e : 0.611145
  EX_so4_e : 0.159546
  EX_k_e : 0.123668
  EX_fe2_e : 0.010176
  EX_mg2_e : 0.005496
  EX_ca2_e : 0.003298
  EX_cl_e : 0.003298
  EX_cu2_e : 0.000449
  EX_mn2_e : 0.000438
  EX_zn2_e : 0.000216
  EX_ni2_e : 0.000205
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 47.169138
  EX_co2_e : 29.095260
  EX_h_e : 6.862583
  EX_ac_e : 0.368855
  DM_oxam_c : 0.269036
  DM_5drib_c : 0.268752
  DM_4crsol_c : 0.268469
  Auxiliary production reaction : 0.134164

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