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 : ditp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (45 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4467 b4382 b4384 b3752 b0871 b2779 b2925 b2097 b2407 b1004 b3713 b1109 b0046 b3236 b1982 b3946 b0825 b1602 b0114 b0529 b2492 b0904 b1380 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.373116 (mmol/gDw/h)
  Minimum Production Rate : 0.075004 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.149800
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.329889
  EX_pi_e : 0.584921
  EX_so4_e : 0.093958
  EX_k_e : 0.072830
  EX_fe2_e : 0.005993
  EX_mg2_e : 0.003237
  EX_ca2_e : 0.001942
  EX_cl_e : 0.001942
  EX_cu2_e : 0.000265
  EX_mn2_e : 0.000258
  EX_zn2_e : 0.000127
  EX_ni2_e : 0.000121

Product: (mmol/gDw/h)
  EX_h2o_e : 44.167782
  EX_co2_e : 28.168000
  EX_h_e : 8.834156
  EX_pyr_e : 5.171265
  EX_glyc__R_e : 0.084041
  Auxiliary production reaction : 0.075004
  DM_oxam_c : 0.000251
  DM_mththf_c : 0.000167
  DM_5drib_c : 0.000084
  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