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 : glx_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b1241 b0351 b4069 b4384 b3752 b3115 b1849 b2296 b2779 b2925 b2097 b2926 b3617 b2407 b2690 b2388 b1982 b3665 b3565 b0261 b3945 b4381 b2406 b0112 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.420517 (mmol/gDw/h)
  Minimum Production Rate : 0.147053 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.437074
  EX_o2_e : 275.367174
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.573451
  EX_pi_e : 0.405633
  EX_so4_e : 0.105895
  EX_k_e : 0.082082
  EX_mg2_e : 0.003648
  EX_ca2_e : 0.002189
  EX_cl_e : 0.002189
  EX_cu2_e : 0.000298
  EX_mn2_e : 0.000291
  EX_zn2_e : 0.000143
  EX_ni2_e : 0.000136
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993246
  EX_h2o_e : 547.445068
  EX_co2_e : 25.715164
  EX_ac_e : 1.513338
  EX_ade_e : 0.806380
  DM_5drib_c : 0.806192
  DM_4crsol_c : 0.806004
  Auxiliary production reaction : 0.147053

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