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 : malcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (14 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b3399 b0586 b3831 b4384 b2744 b3708 b3008 b0910 b3752 b0871 b2883 b0121 b1982 b2797 b3117 b1814 b4471 b1623 b0261 b0411 b4381 b2406 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b3821 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.770150 (mmol/gDw/h)
  Minimum Production Rate : 0.058438 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.630242
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.081986
  EX_pi_e : 0.918204
  EX_so4_e : 0.252377
  EX_k_e : 0.150328
  EX_fe2_e : 0.012369
  EX_mg2_e : 0.006681
  EX_cl_e : 0.004009
  EX_ca2_e : 0.004009
  EX_cu2_e : 0.000546
  EX_mn2_e : 0.000532
  EX_zn2_e : 0.000263
  EX_ni2_e : 0.000249
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.549387
  EX_co2_e : 26.096244
  EX_h_e : 7.665564
  EX_thym_e : 0.177685
  Auxiliary production reaction : 0.058438
  DM_5drib_c : 0.000517
  DM_4crsol_c : 0.000172

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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