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 : dhnpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (78 of 90: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b3553 b1478 b4382 b1241 b4069 b4384 b3708 b3752 b3115 b1849 b2296 b2925 b2097 b2407 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b1033 b2440 b0261 b1602 b2406 b0114 b0509 b3125 b2366 b0529 b2492 b0904 b1533 b3927 b1380 b0494 b2660 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.371812 (mmol/gDw/h)
  Minimum Production Rate : 0.236248 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.451638
  EX_o2_e : 281.764985
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.198864
  EX_pi_e : 0.358653
  EX_so4_e : 0.093630
  EX_k_e : 0.072575
  EX_mg2_e : 0.003225
  EX_ca2_e : 0.001935
  EX_cl_e : 0.001935
  EX_cu2_e : 0.000264
  EX_mn2_e : 0.000257
  EX_zn2_e : 0.000127
  EX_ni2_e : 0.000120

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994028
  EX_h2o_e : 544.150552
  EX_co2_e : 32.157329
  EX_ac_e : 4.942708
  Auxiliary production reaction : 0.236248
  EX_12ppd__R_e : 0.188973
  EX_ade_e : 0.000416
  DM_5drib_c : 0.000249
  DM_4crsol_c : 0.000083

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