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 : dgtp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b3399 b4069 b2502 b4384 b2744 b3708 b2930 b4232 b3697 b3925 b3115 b1849 b2296 b2797 b3117 b1814 b4471 b3946 b0825 b3665 b0675 b2361 b2291 b4381 b0452 b3654 b3714 b3664 b0114 b1539 b2492 b0904 b1533 b3927   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.758852 (mmol/gDw/h)
  Minimum Production Rate : 0.214270 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.742600
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.266887
  EX_pi_e : 1.374804
  EX_so4_e : 0.191094
  EX_k_e : 0.148123
  EX_fe2_e : 0.012188
  EX_mg2_e : 0.006583
  EX_cl_e : 0.003950
  EX_ca2_e : 0.003950
  EX_cu2_e : 0.000538
  EX_mn2_e : 0.000524
  EX_zn2_e : 0.000259
  EX_ni2_e : 0.000245
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.865292
  EX_co2_e : 25.826330
  EX_h_e : 8.057237
  EX_ac_e : 0.441793
  Auxiliary production reaction : 0.214270
  DM_5drib_c : 0.000171
  DM_4crsol_c : 0.000169

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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