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 : glyclt_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (38 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4467 b1478 b4269 b0493 b3588 b3003 b3011 b1241 b0871 b1004 b3713 b1109 b0046 b3236 b1638 b0907 b1779 b4139 b4014 b2976 b1602 b0507 b0452 b0529 b3029 b1380 b2660 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.499333 (mmol/gDw/h)
  Minimum Production Rate : 0.210611 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.816732
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.392752
  EX_pi_e : 0.481659
  EX_so4_e : 0.125742
  EX_k_e : 0.097466
  EX_fe2_e : 0.008020
  EX_mg2_e : 0.004332
  EX_ca2_e : 0.002599
  EX_cl_e : 0.002599
  EX_cu2_e : 0.000354
  EX_mn2_e : 0.000345
  EX_zn2_e : 0.000170
  EX_ni2_e : 0.000161
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 51.656562
  EX_co2_e : 38.470564
  EX_h_e : 5.411577
  EX_for_e : 0.612898
  EX_glyclt_e : 0.210611
  DM_5drib_c : 0.000112
  DM_4crsol_c : 0.000111

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