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 : fpram_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (26 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b2836 b4382 b1241 b0351 b4069 b4384 b2744 b3708 b3115 b1849 b2296 b3617 b2407 b2797 b3117 b1814 b4471 b2406 b0112 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b1539 b2492 b0904 b1533 b3662 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.518906 (mmol/gDw/h)
  Minimum Production Rate : 1.554115 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.216568
  EX_nh4_e : 10.266480
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.054654
  EX_so4_e : 0.130671
  EX_k_e : 0.101287
  EX_fe2_e : 0.008334
  EX_mg2_e : 0.004502
  EX_ca2_e : 0.002701
  EX_cl_e : 0.002701
  EX_cu2_e : 0.000368
  EX_mn2_e : 0.000359
  EX_zn2_e : 0.000177
  EX_ni2_e : 0.000168
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 43.797357
  EX_co2_e : 20.769808
  EX_h_e : 10.624852
  EX_ac_e : 2.748712
  Auxiliary production reaction : 1.554115
  DM_mththf_c : 0.000232
  DM_5drib_c : 0.000117
  DM_4crsol_c : 0.000116

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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