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 : dcmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (97 of 117: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b3553 b4069 b4384 b3708 b3008 b3752 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b2926 b2407 b1238 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b1033 b0595 b0261 b1701 b1805 b0507 b4381 b2406 b0112 b0114 b2366 b0529 b2492 b0904 b2578 b1533 b3927 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.345192 (mmol/gDw/h)
  Minimum Production Rate : 0.438668 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.629320
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.044438
  EX_pi_e : 0.771642
  EX_so4_e : 0.086926
  EX_k_e : 0.067379
  EX_fe2_e : 0.005544
  EX_mg2_e : 0.002995
  EX_ca2_e : 0.001797
  EX_cl_e : 0.001797
  EX_cu2_e : 0.000245
  EX_mn2_e : 0.000239
  EX_zn2_e : 0.000118
  EX_ni2_e : 0.000111

Product: (mmol/gDw/h)
  EX_h2o_e : 44.863120
  EX_co2_e : 27.616166
  EX_h_e : 9.310770
  EX_pyr_e : 4.621262
  Auxiliary production reaction : 0.438668
  EX_ac_e : 0.200966
  DM_oxam_c : 0.000386
  DM_5drib_c : 0.000232
  DM_4crsol_c : 0.000077

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