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 : datp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (96 of 114: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3553 b3399 b3942 b1732 b2502 b2744 b0871 b3115 b1849 b2296 b2779 b2925 b2097 b3844 b1004 b3713 b1109 b0046 b2690 b2210 b1033 b4374 b2361 b2291 b3945 b1602 b1727 b0114 b0529 b2492 b0904 b1380 b1517 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.354050 (mmol/gDw/h)
  Minimum Production Rate : 0.071171 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.397167
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.180519
  EX_pi_e : 0.555032
  EX_so4_e : 0.089157
  EX_k_e : 0.069108
  EX_fe2_e : 0.005686
  EX_mg2_e : 0.003071
  EX_ca2_e : 0.001843
  EX_cl_e : 0.001843
  EX_cu2_e : 0.000251
  EX_mn2_e : 0.000245
  EX_zn2_e : 0.000121
  EX_ni2_e : 0.000114

Product: (mmol/gDw/h)
  EX_h2o_e : 44.106680
  EX_co2_e : 28.260900
  EX_h_e : 8.965378
  EX_pyr_e : 5.497759
  Auxiliary production reaction : 0.071171
  EX_hxan_e : 0.000238
  DM_mththf_c : 0.000159
  DM_5drib_c : 0.000080
  DM_4crsol_c : 0.000079

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