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 : 2omph_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (39 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3752 b4152 b3115 b1849 b2296 b3617 b2407 b1612 b1611 b4122 b0907 b4138 b4123 b0621 b0114 b0529 b2492 b0904 b1511 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.475804 (mmol/gDw/h)
  Minimum Production Rate : 0.228126 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.283939
  EX_o2_e : 267.792487
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.813475
  EX_pi_e : 0.458964
  EX_so4_e : 0.119817
  EX_k_e : 0.092874
  EX_mg2_e : 0.004128
  EX_ca2_e : 0.002477
  EX_cl_e : 0.002477
  EX_cu2_e : 0.000337
  EX_mn2_e : 0.000329
  EX_zn2_e : 0.000162
  EX_ni2_e : 0.000154
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992358
  EX_h2o_e : 539.187196
  EX_co2_e : 21.933714
  EX_ac_e : 1.669380
  EX_succ_e : 0.496165
  EX_ura_e : 0.337416
  DM_mththf_c : 0.228339
  Auxiliary production reaction : 0.228126
  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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