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 : air_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (44 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b0871 b2779 b0030 b2407 b0517 b0907 b1779 b1982 b3616 b3589 b0261 b0505 b4381 b2406 b0112 b0511 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.437293 (mmol/gDw/h)
  Minimum Production Rate : 1.421536 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.934768
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.989299
  EX_pi_e : 1.843352
  EX_so4_e : 0.110119
  EX_k_e : 0.085357
  EX_fe2_e : 0.007023
  EX_mg2_e : 0.003794
  EX_ca2_e : 0.002276
  EX_cl_e : 0.002276
  EX_cu2_e : 0.000310
  EX_mn2_e : 0.000302
  EX_zn2_e : 0.000149
  EX_ni2_e : 0.000141
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 47.193895
  EX_co2_e : 25.691026
  EX_h_e : 8.284691
  EX_acald_e : 2.492041
  Auxiliary production reaction : 1.421536
  EX_xan_e : 0.000489
  DM_5drib_c : 0.000293
  EX_glyc__R_e : 0.000098
  DM_4crsol_c : 0.000098

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