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 : grdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (29 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b1241 b0351 b4069 b4384 b2744 b2297 b2458 b2407 b3124 b1612 b1611 b4122 b3616 b3589 b1623 b3665 b4381 b0114 b0755 b3612 b0529 b2492 b0904 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.511286 (mmol/gDw/h)
  Minimum Production Rate : 0.980208 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.101391
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.523565
  EX_pi_e : 2.453606
  EX_so4_e : 0.128752
  EX_k_e : 0.099799
  EX_fe2_e : 0.008212
  EX_mg2_e : 0.004435
  EX_cl_e : 0.002661
  EX_ca2_e : 0.002661
  EX_cu2_e : 0.000363
  EX_mn2_e : 0.000353
  EX_zn2_e : 0.000174
  EX_ni2_e : 0.000165
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 43.092025
  EX_co2_e : 25.578606
  EX_h_e : 5.534664
  Auxiliary production reaction : 0.980208
  EX_ac_e : 0.747547
  EX_fum_e : 0.533853
  EX_ade_e : 0.000344
  DM_mththf_c : 0.000229
  DM_5drib_c : 0.000115
  DM_4crsol_c : 0.000114

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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