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 : bmoco1gdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (30 of 137: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b4384 b3708 b3008 b3752 b0871 b2407 b1982 b2797 b3117 b1814 b4471 b0261 b0114 b2366 b0755 b3612 b2492 b0904 b1533 b3927 b2835 b2413 b0494 b3447   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.752642 (mmol/gDw/h)
  Minimum Production Rate : 0.030487 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.615387
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.585771
  EX_pi_e : 0.817463
  EX_so4_e : 0.311477
  EX_k_e : 0.146910
  EX_mobd_e : 0.030492
  EX_fe2_e : 0.012088
  EX_mg2_e : 0.006529
  EX_ca2_e : 0.003918
  EX_cl_e : 0.003918
  EX_cu2_e : 0.000534
  EX_mn2_e : 0.000520
  EX_zn2_e : 0.000257
  EX_ni2_e : 0.000243
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 49.407832
  EX_co2_e : 28.191222
  EX_h_e : 7.007036
  Auxiliary production reaction : 0.030487
  DM_5drib_c : 0.000505
  DM_4crsol_c : 0.000168

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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