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 : 10fthf_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (20 of 46: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3553 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3752 b0871 b2407 b0121 b1982 b3616 b3589 b1033 b4014 b0261 b2976 b4381 b2406 b0112 b0114 b0509 b3125 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.348130 (mmol/gDw/h)
  Minimum Production Rate : 1.131686 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.434953
  EX_nh4_e : 11.681966
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.335808
  EX_so4_e : 0.087666
  EX_k_e : 0.067952
  EX_fe2_e : 0.005591
  EX_mg2_e : 0.003020
  EX_ca2_e : 0.001812
  EX_cl_e : 0.001812
  EX_cu2_e : 0.000247
  EX_mn2_e : 0.000241
  EX_zn2_e : 0.000119
  EX_ni2_e : 0.000112

Product: (mmol/gDw/h)
  EX_h2o_e : 48.631390
  EX_co2_e : 17.935425
  EX_h_e : 14.516631
  EX_acald_e : 1.438163
  EX_glyclt_e : 1.131919
  Auxiliary production reaction : 1.131686
  DM_oxam_c : 0.000390
  DM_5drib_c : 0.000234
  DM_4crsol_c : 0.000078

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