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_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (82 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 52
  Gene deletion: b3553 b1478 b1241 b4069 b4384 b2744 b3708 b3752 b2297 b2458 b2779 b2926 b2407 b1004 b3713 b1109 b0046 b3236 b1982 b2797 b3117 b1814 b4471 b1033 b4374 b2361 b2291 b0261 b0411 b2799 b3945 b1602 b3709 b2913 b3161 b0112 b3915 b2366 b2492 b0904 b1533 b3821 b1380 b1473 b1695 b4141 b1798 b3662 b0606 b2285 b1011 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.375263 (mmol/gDw/h)
  Minimum Production Rate : 0.208515 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.406452
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.139802
  EX_pi_e : 0.361981
  EX_so4_e : 0.094500
  EX_k_e : 0.073249
  EX_fe3_e : 0.006029
  EX_mg2_e : 0.003255
  EX_ca2_e : 0.001953
  EX_cl_e : 0.001953
  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_h2o_e : 50.226646
  EX_co2_e : 34.895080
  EX_h_e : 6.742104
  EX_ac_e : 0.992527
  EX_ade_e : 0.417398
  DM_5drib_c : 0.417230
  DM_4crsol_c : 0.417062
  EX_glyc__R_e : 0.208489

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