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 : dnad_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (38 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b2297 b2458 b2883 b1779 b1982 b3616 b3589 b4374 b0675 b2361 b2291 b0261 b0507 b4381 b0112 b2868 b4064 b4464 b0114 b0529 b2492 b0904 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.320890 (mmol/gDw/h)
  Minimum Production Rate : 0.614977 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 32.903979
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.157242
  EX_pi_e : 1.539487
  EX_so4_e : 0.080807
  EX_k_e : 0.062635
  EX_fe2_e : 0.005154
  EX_mg2_e : 0.002784
  EX_cl_e : 0.001670
  EX_ca2_e : 0.001670
  EX_cu2_e : 0.000228
  EX_mn2_e : 0.000222
  EX_zn2_e : 0.000109
  EX_ni2_e : 0.000104

Product: (mmol/gDw/h)
  EX_h2o_e : 52.519849
  EX_co2_e : 31.742900
  EX_h_e : 6.494674
  EX_ac_e : 1.084291
  Auxiliary production reaction : 0.614977
  EX_ade_e : 0.000359
  DM_5drib_c : 0.000215
  EX_glyclt_e : 0.000215
  DM_4crsol_c : 0.000072

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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