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 : dhmpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (111 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 52
  Gene deletion: b4467 b1478 b3399 b4382 b1241 b4069 b2502 b4384 b2744 b2297 b2458 b2779 b2926 b1004 b3713 b1109 b0046 b3236 b1638 b0907 b0207 b3012 b1982 b4139 b0675 b2361 b4014 b0261 b2976 b2799 b1602 b4381 b2789 b3127 b3915 b2975 b0114 b3603 b0529 b2492 b0904 b2954 b1781 b3001 b3029 b1380 b0325 b2660 b1771 b0221 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.388951 (mmol/gDw/h)
  Minimum Production Rate : 0.541980 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.663282
  EX_o2_e : 288.679872
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.458011
  EX_pi_e : 0.375185
  EX_so4_e : 0.097946
  EX_k_e : 0.075921
  EX_mg2_e : 0.003374
  EX_ca2_e : 0.002024
  EX_cl_e : 0.002024
  EX_cu2_e : 0.000276
  EX_mn2_e : 0.000269
  EX_zn2_e : 0.000133
  EX_ni2_e : 0.000126

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993753
  EX_h2o_e : 554.120231
  EX_co2_e : 37.882779
  Auxiliary production reaction : 0.541980
  EX_ac_e : 0.499088
  EX_urea_e : 0.272646
  EX_ade_e : 0.000435
  DM_5drib_c : 0.000261
  EX_dxylnt_e : 0.000173
  DM_4crsol_c : 0.000087

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