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 (36 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b1241 b0351 b4069 b4384 b3115 b1849 b2296 b1850 b3617 b0030 b2407 b0517 b1779 b1982 b0261 b4381 b2406 b0112 b0511 b0114 b0509 b3125 b0529 b2492 b0904 b0508 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.429106 (mmol/gDw/h)
  Minimum Production Rate : 0.892482 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.035325
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.311750
  EX_pi_e : 1.306400
  EX_so4_e : 0.108057
  EX_k_e : 0.083758
  EX_fe2_e : 0.006892
  EX_mg2_e : 0.003722
  EX_ca2_e : 0.002233
  EX_cl_e : 0.002233
  EX_cu2_e : 0.000304
  EX_mn2_e : 0.000297
  EX_zn2_e : 0.000146
  EX_ni2_e : 0.000139
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 44.141653
  EX_co2_e : 24.541921
  EX_h_e : 10.161939
  EX_ac_e : 1.896194
  Auxiliary production reaction : 0.892482
  EX_glyclt_e : 0.753024
  DM_5drib_c : 0.376416
  DM_4crsol_c : 0.376224

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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