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 : prbamp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (32 of 47: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4467 b1478 b1241 b4069 b4384 b3752 b2297 b2458 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b0261 b0411 b2799 b3945 b1602 b0153 b4381 b0584 b0529 b2492 b0904 b1380 b2660 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.375015 (mmol/gDw/h)
  Minimum Production Rate : 0.589813 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.716268
  EX_o2_e : 285.000613
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.001301
  EX_pi_e : 1.541369
  EX_so4_e : 0.094436
  EX_k_e : 0.073200
  EX_mg2_e : 0.003253
  EX_ca2_e : 0.001952
  EX_cl_e : 0.001952
  EX_cu2_e : 0.000266
  EX_mn2_e : 0.000259
  EX_zn2_e : 0.000128
  EX_ni2_e : 0.000121

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993977
  EX_h2o_e : 552.157394
  EX_co2_e : 33.995699
  EX_glyclt_e : 0.662422
  Auxiliary production reaction : 0.589813
  EX_ac_e : 0.218329
  EX_ade_e : 0.000420
  DM_5drib_c : 0.000252
  DM_4crsol_c : 0.000084

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