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 : bwco1gdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 96: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b1241 b0351 b4069 b4384 b3708 b2297 b2458 b0030 b2407 b3844 b1238 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b0261 b0507 b4381 b2406 b0112 b0452 b2975 b0114 b3603 b2366 b2492 b0904 b1533 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.504274 (mmol/gDw/h)
  Minimum Production Rate : 0.251483 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.074768
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.218932
  EX_pi_e : 1.240876
  EX_so4_e : 1.132919
  EX_tungs_e : 0.251483
  EX_k_e : 0.098431
  EX_fe2_e : 0.008099
  EX_mg2_e : 0.004375
  EX_ca2_e : 0.002625
  EX_cl_e : 0.002625
  EX_cu2_e : 0.000358
  EX_mn2_e : 0.000348
  EX_zn2_e : 0.000172
  EX_ni2_e : 0.000163
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 48.281562
  EX_co2_e : 23.898682
  EX_h_e : 9.317264
  EX_ac_e : 3.928212
  Auxiliary production reaction : 0.251483
  DM_oxam_c : 0.000564
  DM_5drib_c : 0.000338
  DM_4crsol_c : 0.000112

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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