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 : thmnp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (41 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3399 b4069 b2502 b2744 b3708 b3008 b3115 b1849 b2296 b2779 b1982 b2797 b3117 b1814 b4471 b2440 b4374 b0675 b2361 b2291 b0261 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b0494   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.642835 (mmol/gDw/h)
  Minimum Production Rate : 0.408455 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.633490
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.984838
  EX_pi_e : 0.620083
  EX_so4_e : 0.161879
  EX_k_e : 0.125477
  EX_fe2_e : 0.010325
  EX_mg2_e : 0.005577
  EX_cl_e : 0.003346
  EX_ca2_e : 0.003346
  EX_cu2_e : 0.000456
  EX_mn2_e : 0.000444
  EX_zn2_e : 0.000219
  EX_ni2_e : 0.000208
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 49.840138
  EX_co2_e : 29.188547
  EX_h_e : 8.323149
  Auxiliary production reaction : 0.408455
  EX_ac_e : 0.374250
  DM_5drib_c : 0.000431
  DM_4crsol_c : 0.000143

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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