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 : preq1_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (85 of 95: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3500 b3553 b3399 b4382 b0238 b0125 b0474 b2518 b1241 b0351 b4069 b4384 b2744 b2297 b2458 b2781 b0099 b3617 b0160 b2235 b1982 b0477 b1033 b0675 b2361 b0261 b0411 b0507 b2406 b0112 b2868 b4064 b4464 b0114 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.447092 (mmol/gDw/h)
  Minimum Production Rate : 1.713678 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 984.946003
  EX_o2_e : 273.959366
  EX_nh4_e : 13.399445
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.431267
  EX_so4_e : 0.112587
  EX_k_e : 0.087269
  EX_mg2_e : 0.003879
  EX_ca2_e : 0.002327
  EX_cl_e : 0.002327
  EX_cu2_e : 0.000317
  EX_mn2_e : 0.000309
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992819
  EX_h2o_e : 550.431257
  EX_co2_e : 21.486607
  EX_ac_e : 4.081245
  Auxiliary production reaction : 1.713678
  EX_ade_e : 0.000500
  DM_5drib_c : 0.000300
  EX_glyclt_e : 0.000299
  DM_4crsol_c : 0.000100

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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