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 : dhnpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (33 of 90: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b3115 b1849 b2296 b2779 b0160 b0517 b1982 b3616 b3589 b0675 b2361 b2291 b0261 b0507 b4381 b0112 b0114 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.479958 (mmol/gDw/h)
  Minimum Production Rate : 0.706395 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.360945
  EX_nh4_e : 10.984146
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.462970
  EX_so4_e : 0.120863
  EX_k_e : 0.093684
  EX_fe2_e : 0.007709
  EX_mg2_e : 0.004164
  EX_ca2_e : 0.002498
  EX_cl_e : 0.002498
  EX_cu2_e : 0.000340
  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 : 48.589346
  EX_co2_e : 22.050396
  EX_h_e : 10.491448
  EX_thymd_e : 1.130585
  Auxiliary production reaction : 0.706395
  EX_ac_e : 0.279425
  EX_alltn_e : 0.001874
  DM_5drib_c : 0.001659
  DM_4crsol_c : 0.001444
  EX_glyclt_e : 0.001337

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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