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 : ade_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (114 of 133: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3553 b1241 b0351 b4069 b3115 b1849 b2296 b3617 b2407 b1004 b3713 b1109 b0046 b3236 b1033 b4381 b2868 b4064 b4464 b0114 b0529 b2492 b0904 b1380 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.475167 (mmol/gDw/h)
  Minimum Production Rate : 0.012753 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 34.441148
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.789650
  EX_pi_e : 0.458349
  EX_so4_e : 0.119657
  EX_k_e : 0.092749
  EX_fe2_e : 0.007632
  EX_mg2_e : 0.004122
  EX_ca2_e : 0.002473
  EX_cl_e : 0.002473
  EX_cu2_e : 0.000337
  EX_mn2_e : 0.000328
  EX_zn2_e : 0.000162
  EX_ni2_e : 0.000153
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 53.489842
  EX_co2_e : 32.727691
  EX_h_e : 9.629612
  EX_ac_e : 1.605701
  EX_xan_e : 0.898530
  EX_ade_e : 0.012753
  DM_mththf_c : 0.000213
  DM_5drib_c : 0.000107
  DM_4crsol_c : 0.000106

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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