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 : dgsn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (32 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b4069 b4384 b3708 b3752 b2297 b2458 b2407 b2797 b3117 b1814 b4471 b3665 b3654 b3714 b3664 b0114 b2366 b2492 b0904 b1533 b3927 b3825 b0494 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.763275 (mmol/gDw/h)
  Minimum Production Rate : 0.243217 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.327663
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.459387
  EX_pi_e : 0.736259
  EX_so4_e : 0.192208
  EX_k_e : 0.148986
  EX_fe2_e : 0.012259
  EX_mg2_e : 0.006621
  EX_ca2_e : 0.003973
  EX_cl_e : 0.003973
  EX_cu2_e : 0.000541
  EX_mn2_e : 0.000527
  EX_zn2_e : 0.000260
  EX_ni2_e : 0.000247
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.179826
  EX_co2_e : 25.348465
  EX_h_e : 8.673725
  EX_ac_e : 0.444368
  Auxiliary production reaction : 0.243217
  DM_mththf_c : 0.000342
  DM_5drib_c : 0.000172
  DM_4crsol_c : 0.000170

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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