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 : thmnp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (40 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b3752 b0871 b3617 b2883 b1982 b0261 b0507 b4381 b2406 b0112 b2868 b4064 b4464 b2975 b0114 b3603 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.478012 (mmol/gDw/h)
  Minimum Production Rate : 1.553901 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.542321
  EX_nh4_e : 12.934664
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.461093
  EX_so4_e : 0.120373
  EX_k_e : 0.093304
  EX_fe2_e : 0.007677
  EX_mg2_e : 0.004147
  EX_ca2_e : 0.002488
  EX_cl_e : 0.002488
  EX_cu2_e : 0.000339
  EX_mn2_e : 0.000330
  EX_zn2_e : 0.000163
  EX_ni2_e : 0.000154
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 49.054316
  EX_co2_e : 22.440894
  EX_h_e : 12.164341
  EX_acald_e : 1.975039
  Auxiliary production reaction : 1.553901
  EX_ade_e : 0.000535
  DM_5drib_c : 0.000321
  DM_4crsol_c : 0.000107

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