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 : 5pg35pg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (44 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b1241 b0351 b4069 b2502 b2744 b3115 b1849 b2296 b3617 b2883 b0517 b1982 b1623 b3665 b0675 b2361 b0507 b4388 b4381 b0114 b0529 b2492 b0904 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.555667 (mmol/gDw/h)
  Minimum Production Rate : 0.525376 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.136677
  EX_nh4_e : 11.314944
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.586752
  EX_so4_e : 0.139928
  EX_k_e : 0.108462
  EX_fe2_e : 0.008925
  EX_mg2_e : 0.004820
  EX_ca2_e : 0.002892
  EX_cl_e : 0.002892
  EX_cu2_e : 0.000394
  EX_mn2_e : 0.000384
  EX_zn2_e : 0.000189
  EX_ni2_e : 0.000179
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 49.039028
  EX_co2_e : 21.125482
  EX_h_e : 12.643181
  EX_ac_e : 2.748707
  Auxiliary production reaction : 0.525376
  EX_alltn_e : 0.014540
  EX_ade_e : 0.000374
  EX_glyclt_e : 0.000372
  DM_mththf_c : 0.000249
  DM_5drib_c : 0.000125
  DM_4crsol_c : 0.000124

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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