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 : aps_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (33 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b1241 b0351 b3831 b4069 b2744 b2297 b2458 b0160 b0517 b0907 b1779 b1982 b3616 b3589 b0675 b2361 b0261 b0507 b4381 b0112 b0114 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.492992 (mmol/gDw/h)
  Minimum Production Rate : 0.931907 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.831248
  EX_nh4_e : 10.037610
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.407450
  EX_so4_e : 1.056052
  EX_k_e : 0.096229
  EX_fe2_e : 0.007918
  EX_mg2_e : 0.004277
  EX_ca2_e : 0.002566
  EX_cl_e : 0.002566
  EX_cu2_e : 0.000350
  EX_mn2_e : 0.000341
  EX_zn2_e : 0.000168
  EX_ni2_e : 0.000159
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 50.740683
  EX_co2_e : 25.513183
  EX_h_e : 9.818227
  EX_ac_e : 2.438675
  Auxiliary production reaction : 0.931907
  EX_alltn_e : 0.013451
  DM_5drib_c : 0.000331
  EX_glyclt_e : 0.000220
  DM_4crsol_c : 0.000110

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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