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 : xmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (83 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 52
  Gene deletion: b4467 b1478 b1241 b0351 b3831 b4069 b4384 b3614 b0910 b3752 b3115 b1849 b2296 b2781 b3617 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b1759 b0937 b1982 b4139 b1623 b4015 b0261 b1701 b1805 b2799 b3945 b1602 b2913 b4381 b2406 b2975 b3603 b0529 b2492 b0904 b1300 b2954 b3029 b1380 b3918 b4042 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.417592 (mmol/gDw/h)
  Minimum Production Rate : 0.362564 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.944610
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.962086
  EX_pi_e : 0.765376
  EX_so4_e : 0.105158
  EX_k_e : 0.081511
  EX_mg2_e : 0.003623
  EX_fe2_e : 0.003446
  EX_fe3_e : 0.003261
  EX_ca2_e : 0.002174
  EX_cl_e : 0.002174
  EX_cu2_e : 0.000296
  EX_mn2_e : 0.000289
  EX_zn2_e : 0.000142
  EX_ni2_e : 0.000135
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 50.766045
  EX_co2_e : 35.747808
  EX_h_e : 6.996118
  EX_ac_e : 1.628142
  Auxiliary production reaction : 0.362564
  EX_3hpp_e : 0.075585
  EX_hxan_e : 0.000467
  DM_5drib_c : 0.000280
  DM_4crsol_c : 0.000093

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