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 : didp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (44 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b1241 b0351 b4069 b2744 b3708 b2297 b2458 b3617 b2883 b2797 b3117 b1814 b4471 b4381 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b1539 b2492 b0904 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.643785 (mmol/gDw/h)
  Minimum Production Rate : 0.642726 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 22.809086
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.523722
  EX_pi_e : 1.906450
  EX_so4_e : 0.162118
  EX_k_e : 0.125662
  EX_fe2_e : 0.010340
  EX_mg2_e : 0.005585
  EX_ca2_e : 0.003351
  EX_cl_e : 0.003351
  EX_cu2_e : 0.000456
  EX_mn2_e : 0.000445
  EX_zn2_e : 0.000220
  EX_ni2_e : 0.000208
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 47.610763
  EX_co2_e : 22.897484
  EX_h_e : 9.968235
  EX_ac_e : 2.124709
  Auxiliary production reaction : 0.642726
  DM_mththf_c : 0.000288
  DM_5drib_c : 0.000145
  DM_4crsol_c : 0.000144

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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