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 : dcyt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (39 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b3553 b1478 b1241 b0351 b4384 b2930 b4232 b3697 b3925 b0871 b2926 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b2690 b0207 b3012 b1982 b1033 b0261 b2799 b1602 b2913 b4381 b2406 b3915 b0529 b2492 b0904 b1781 b3001 b3927 b3821 b1380 b0325 b1695 b1771 b3662 b0606 b2285 b1011 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.368371 (mmol/gDw/h)
  Minimum Production Rate : 0.095937 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.328124
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.268187
  EX_pi_e : 0.355333
  EX_so4_e : 0.092764
  EX_k_e : 0.071904
  EX_fe3_e : 0.005918
  EX_mg2_e : 0.003196
  EX_ca2_e : 0.001917
  EX_cl_e : 0.001917
  EX_cu2_e : 0.000261
  EX_mn2_e : 0.000255
  EX_zn2_e : 0.000126
  EX_ni2_e : 0.000119

Product: (mmol/gDw/h)
  EX_h2o_e : 44.018109
  EX_co2_e : 28.419839
  EX_h_e : 8.878497
  EX_pyr_e : 5.198029
  Auxiliary production reaction : 0.095915
  EX_ade_e : 0.000412
  DM_5drib_c : 0.000247
  DM_4crsol_c : 0.000082

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