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 : 5caiz_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (27 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3752 b0871 b2926 b3617 b2407 b1982 b3665 b0261 b0507 b2406 b0112 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.452182 (mmol/gDw/h)
  Minimum Production Rate : 1.469935 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.512652
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.295857
  EX_pi_e : 1.906112
  EX_so4_e : 0.113868
  EX_k_e : 0.088263
  EX_fe2_e : 0.007262
  EX_mg2_e : 0.003923
  EX_cl_e : 0.002354
  EX_ca2_e : 0.002354
  EX_cu2_e : 0.000321
  EX_mn2_e : 0.000312
  EX_zn2_e : 0.000154
  EX_ni2_e : 0.000146
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 48.175842
  EX_co2_e : 24.470439
  EX_h_e : 10.037396
  EX_acald_e : 1.868014
  Auxiliary production reaction : 1.469935
  EX_ade_e : 0.000506
  DM_5drib_c : 0.000303
  EX_glyclt_e : 0.000303
  DM_4crsol_c : 0.000101

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
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