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 : dhpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (22 of 115: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3553 b3399 b1241 b0351 b4069 b2744 b2297 b2458 b3617 b0160 b1982 b1033 b0675 b2361 b4014 b0261 b2976 b0507 b4381 b2406 b0112 b0114 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.366516 (mmol/gDw/h)
  Minimum Production Rate : 1.385656 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 22.291668
  EX_nh4_e : 12.282280
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.353544
  EX_so4_e : 0.092296
  EX_k_e : 0.071541
  EX_fe2_e : 0.005887
  EX_mg2_e : 0.003180
  EX_ca2_e : 0.001908
  EX_cl_e : 0.001908
  EX_cu2_e : 0.000260
  EX_mn2_e : 0.000253
  EX_zn2_e : 0.000125
  EX_ni2_e : 0.000118

Product: (mmol/gDw/h)
  EX_h2o_e : 50.770987
  EX_co2_e : 18.901811
  EX_h_e : 16.404482
  EX_ac_e : 1.931290
  EX_glyclt_e : 1.385901
  Auxiliary production reaction : 1.385656
  DM_oxam_c : 0.010000
  DM_5drib_c : 0.000246
  DM_4crsol_c : 0.000082

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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