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 : 2h3oppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b1241 b0351 b4069 b4384 b3708 b3115 b1849 b2296 b3617 b0030 b2407 b1238 b3124 b1982 b2797 b3117 b1814 b4471 b0261 b4381 b2406 b0112 b0114 b2366 b2492 b0904 b1533 b3821 b0514 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.527102 (mmol/gDw/h)
  Minimum Production Rate : 0.394499 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.008870
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.481892
  EX_pi_e : 0.508446
  EX_so4_e : 0.132735
  EX_k_e : 0.102887
  EX_fe2_e : 0.008466
  EX_mg2_e : 0.004573
  EX_ca2_e : 0.002744
  EX_cl_e : 0.002744
  EX_cu2_e : 0.000374
  EX_mn2_e : 0.000364
  EX_zn2_e : 0.000180
  EX_ni2_e : 0.000170
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 40.390983
  EX_co2_e : 22.132773
  EX_h_e : 8.818808
  EX_ac_e : 2.002616
  DM_oxam_c : 0.789235
  DM_5drib_c : 0.788998
  DM_4crsol_c : 0.788762
  Auxiliary production reaction : 0.394499

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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