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 : bmoco1gdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (90 of 137: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b1241 b0351 b4069 b4384 b2744 b3708 b3752 b2297 b2458 b3617 b2407 b1982 b2797 b3117 b1814 b4471 b4374 b2361 b2291 b0261 b0507 b2406 b0112 b0452 b2975 b0114 b3603 b1539 b2492 b0904 b1533 b3662 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.504265 (mmol/gDw/h)
  Minimum Production Rate : 0.251479 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.074465
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.218762
  EX_pi_e : 1.240853
  EX_so4_e : 1.132898
  EX_mobd_e : 0.251482
  EX_k_e : 0.098429
  EX_mg2_e : 0.004374
  EX_fe2_e : 0.004162
  EX_fe3_e : 0.003937
  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 : 48.279810
  EX_co2_e : 23.899348
  EX_h_e : 9.321029
  EX_ac_e : 3.928139
  Auxiliary production reaction : 0.251479
  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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