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 : didp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3553 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b0871 b3617 b3236 b2883 b3962 b2210 b4267 b1033 b4388 b4381 b2868 b4064 b4464 b0114 b0509 b3125 b0755 b3612 b0529 b2492 b0904 b0325 b4266 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.429001 (mmol/gDw/h)
  Minimum Production Rate : 0.457568 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.620721
  EX_o2_e : 283.986787
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.521010
  EX_pi_e : 1.328952
  EX_so4_e : 0.108031
  EX_k_e : 0.083738
  EX_mg2_e : 0.003722
  EX_ca2_e : 0.002233
  EX_cl_e : 0.002233
  EX_cu2_e : 0.000304
  EX_mn2_e : 0.000296
  EX_zn2_e : 0.000146
  EX_ni2_e : 0.000139
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993110
  EX_h2o_e : 551.650522
  EX_co2_e : 34.719297
  EX_acald_e : 1.518709
  Auxiliary production reaction : 0.457568
  EX_ade_e : 0.011514
  EX_glyclt_e : 0.000287
  DM_mththf_c : 0.000192
  DM_5drib_c : 0.000097
  DM_4crsol_c : 0.000096

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