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 : glyc__R_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (49 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b2836 b3399 b2502 b2744 b3708 b3008 b0871 b1238 b3124 b1982 b2797 b3117 b1814 b4471 b3449 b0675 b2361 b0261 b4381 b2239 b2406 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b0594 b1600 b0514 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.756989 (mmol/gDw/h)
  Minimum Production Rate : 0.024079 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.533622
  EX_o2_e : 274.383600
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.601159
  EX_pi_e : 0.730257
  EX_so4_e : 0.190625
  EX_k_e : 0.147759
  EX_mg2_e : 0.006567
  EX_ca2_e : 0.003940
  EX_cl_e : 0.003940
  EX_cu2_e : 0.000537
  EX_mn2_e : 0.000523
  EX_zn2_e : 0.000258
  EX_ni2_e : 0.000245
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_fe3_e : 999.987842
  EX_h2o_e : 547.840389
  EX_co2_e : 26.107237
  EX_trp__L_e : 0.188337
  DM_oxam_c : 0.049004
  DM_5drib_c : 0.048665
  DM_4crsol_c : 0.048326
  EX_glyc__R_e : 0.024079
  EX_g3pe_e : 0.000061

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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