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 : preq0_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (37 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b0871 b0030 b2407 b1982 b3616 b3589 b0261 b4381 b2406 b0112 b2975 b0114 b3603 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 : 0.480962 (mmol/gDw/h)
  Minimum Production Rate : 1.563493 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.100097
  EX_nh4_e : 13.012355
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.463939
  EX_so4_e : 0.121116
  EX_k_e : 0.093880
  EX_fe2_e : 0.007725
  EX_mg2_e : 0.004172
  EX_ca2_e : 0.002503
  EX_cl_e : 0.002503
  EX_cu2_e : 0.000341
  EX_mn2_e : 0.000332
  EX_zn2_e : 0.000164
  EX_ni2_e : 0.000155
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 53.674538
  EX_co2_e : 22.210662
  EX_h_e : 12.237815
  EX_acald_e : 3.550724
  Auxiliary production reaction : 1.563493
  DM_oxam_c : 0.000538
  DM_5drib_c : 0.000323
  DM_4crsol_c : 0.000107

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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