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 : 2p4c2me_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (89 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3916 b0469 b0474 b2518 b3831 b4152 b2781 b0030 b1851 b1612 b1611 b4122 b0651 b2162 b1759 b1200 b4161 b4138 b4123 b0621 b4381 b2406 b1723 b0529 b3821 b3918 b1912 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.667513 (mmol/gDw/h)
  Minimum Production Rate : 0.352993 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.868210
  EX_o2_e : 273.669171
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.509711
  EX_pi_e : 1.702867
  EX_so4_e : 0.168093
  EX_k_e : 0.130294
  EX_mg2_e : 0.005791
  EX_ca2_e : 0.003474
  EX_cl_e : 0.003474
  EX_cu2_e : 0.000473
  EX_mn2_e : 0.000461
  EX_zn2_e : 0.000228
  EX_ni2_e : 0.000216
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989279
  EX_h2o_e : 546.842734
  EX_co2_e : 24.390346
  EX_succ_e : 0.696527
  Auxiliary production reaction : 0.352993
  EX_ura_e : 0.120822
  DM_5drib_c : 0.000150
  DM_4crsol_c : 0.000149

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