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

Gene deletion strategy (52 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b2836 b3399 b1241 b0351 b4069 b4384 b2744 b3708 b3115 b1849 b2296 b3617 b0160 b1982 b2797 b3117 b1814 b4471 b3665 b4374 b0675 b2361 b2291 b0261 b0507 b0112 b0114 b1539 b2492 b0904 b1533   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.509155 (mmol/gDw/h)
  Minimum Production Rate : 1.523544 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.954472
  EX_nh4_e : 10.072308
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.014677
  EX_so4_e : 0.128215
  EX_k_e : 0.099383
  EX_fe2_e : 0.008178
  EX_mg2_e : 0.004417
  EX_ca2_e : 0.002650
  EX_cl_e : 0.002650
  EX_cu2_e : 0.000361
  EX_mn2_e : 0.000352
  EX_zn2_e : 0.000174
  EX_ni2_e : 0.000164
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 45.631868
  EX_co2_e : 19.992450
  EX_h_e : 13.471944
  EX_ac_e : 2.696263
  Auxiliary production reaction : 1.523544
  EX_ade_e : 0.000570
  DM_5drib_c : 0.000342
  EX_glyclt_e : 0.000341
  DM_4crsol_c : 0.000114

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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