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 : preq1_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (53 of 95: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b2836 b4384 b3708 b3008 b3752 b0871 b2407 b1982 b2797 b3117 b1814 b4471 b3665 b4381 b2406 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b4141 b1798 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.780585 (mmol/gDw/h)
  Minimum Production Rate : 0.179574 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.094213
  EX_o2_e : 275.390714
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.330749
  EX_pi_e : 0.752957
  EX_so4_e : 0.196567
  EX_k_e : 0.152365
  EX_mg2_e : 0.006772
  EX_ca2_e : 0.004063
  EX_cl_e : 0.004063
  EX_cu2_e : 0.000553
  EX_mn2_e : 0.000539
  EX_zn2_e : 0.000266
  EX_ni2_e : 0.000252
  EX_cobalt2_e : 0.000020

Product: (mmol/gDw/h)
  EX_fe3_e : 999.987463
  EX_h2o_e : 549.106991
  EX_co2_e : 26.699173
  Auxiliary production reaction : 0.179574
  EX_ade_e : 0.000525
  EX_mththf_e : 0.000350
  DM_5drib_c : 0.000176
  DM_4crsol_c : 0.000174

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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