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 : dgsn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b2836 b3399 b4382 b4384 b2744 b1278 b3708 b3008 b0871 b2779 b2925 b2097 b2407 b3236 b2690 b2797 b3117 b1814 b4471 b2210 b0675 b0822 b2868 b1727 b0114 b2366 b2492 b0904 b1533 b3927   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.644150 (mmol/gDw/h)
  Minimum Production Rate : 0.111107 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.648939
  EX_o2_e : 276.688240
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.514464
  EX_pi_e : 0.621351
  EX_so4_e : 0.162210
  EX_k_e : 0.125734
  EX_mg2_e : 0.005588
  EX_cl_e : 0.003353
  EX_ca2_e : 0.003353
  EX_cu2_e : 0.000457
  EX_mn2_e : 0.000445
  EX_zn2_e : 0.000220
  EX_ni2_e : 0.000208
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989654
  EX_h2o_e : 545.086001
  EX_co2_e : 26.854450
  EX_glyc__R_e : 1.864309
  Auxiliary production reaction : 0.111107
  EX_ade_e : 0.000434
  DM_5drib_c : 0.000145
  DM_4crsol_c : 0.000144

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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