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 : ade_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (53 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b4069 b4384 b2744 b3708 b2297 b2458 b2407 b2797 b3117 b1814 b4471 b2440 b0261 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b2366 b2492 b0904 b1533   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.773706 (mmol/gDw/h)
  Minimum Production Rate : 0.328606 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.784983
  EX_o2_e : 274.866309
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.998989
  EX_pi_e : 0.746322
  EX_so4_e : 0.194835
  EX_k_e : 0.151022
  EX_mg2_e : 0.006712
  EX_cl_e : 0.004027
  EX_ca2_e : 0.004027
  EX_cu2_e : 0.000549
  EX_mn2_e : 0.000535
  EX_zn2_e : 0.000264
  EX_ni2_e : 0.000250
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_fe3_e : 999.987574
  EX_h2o_e : 549.410290
  EX_co2_e : 25.699006
  EX_ac_e : 0.450441
  Auxiliary production reaction : 0.328606
  DM_5drib_c : 0.000174
  DM_4crsol_c : 0.000173

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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