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 : glyc_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (6 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4467 b1241 b0351 b3926 b0871 b2925 b2097 b1004 b3713 b1109 b0046 b3236 b3946 b0825 b1493 b3517 b4015 b3945 b1602 b2492 b0904 b1380 b2660 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.445513 (mmol/gDw/h)
  Minimum Production Rate : 3.583135 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.899294
  EX_o2_e : 278.220245
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.811502
  EX_pi_e : 0.429744
  EX_so4_e : 0.112189
  EX_k_e : 0.086961
  EX_mg2_e : 0.003865
  EX_ca2_e : 0.002319
  EX_cl_e : 0.002319
  EX_cu2_e : 0.000316
  EX_mn2_e : 0.000308
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992845
  EX_h2o_e : 539.142387
  EX_co2_e : 30.964335
  EX_glyc_e : 3.583135
  DM_5drib_c : 0.000100
  DM_4crsol_c : 0.000099

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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