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 : gsn_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (46 of 49: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b3942 b1732 b1241 b0351 b4069 b4384 b1479 b3752 b2297 b2458 b2407 b3236 b1779 b2463 b3962 b1982 b3616 b3589 b2210 b4267 b3551 b1014 b0261 b3945 b2913 b4219 b1832 b1778 b4381 b2406 b0112 b0114 b0529 b0306 b3605 b2492 b0904 b1380 b0325 b1710 b2480 b0508 b4266 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.358831 (mmol/gDw/h)
  Minimum Production Rate : 0.469725 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.700433
  EX_o2_e : 286.030472
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.096879
  EX_pi_e : 0.346131
  EX_so4_e : 0.090361
  EX_k_e : 0.070041
  EX_mg2_e : 0.003113
  EX_cl_e : 0.001868
  EX_ca2_e : 0.001868
  EX_cu2_e : 0.000254
  EX_mn2_e : 0.000248
  EX_zn2_e : 0.000122
  EX_ni2_e : 0.000116

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994237
  EX_h2o_e : 551.664477
  EX_co2_e : 34.842734
  EX_ac_e : 1.774945
  EX_gsn_e : 0.469885
  EX_ins_e : 0.217966
  DM_oxam_c : 0.000241
  DM_5drib_c : 0.000081
  DM_4crsol_c : 0.000080

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