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 : grdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (39 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b4467 b4069 b3115 b1849 b2296 b3844 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b0261 b3945 b1602 b2913 b4381 b1727 b0114 b0755 b3612 b0529 b2492 b0904 b1380 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.437872 (mmol/gDw/h)
  Minimum Production Rate : 0.303847 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 999.681160
  EX_h_e : 994.786494
  EX_o2_e : 284.877959
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.728976
  EX_pi_e : 1.030067
  EX_so4_e : 0.110265
  EX_k_e : 0.085469
  EX_mg2_e : 0.003799
  EX_ca2_e : 0.002279
  EX_cl_e : 0.002279
  EX_cu2_e : 0.000310
  EX_mn2_e : 0.000303
  EX_zn2_e : 0.000149
  EX_ni2_e : 0.000141
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.674127
  EX_h2o_e : 549.877433
  EX_co2_e : 36.652632
  EX_fum_e : 0.456609
  Auxiliary production reaction : 0.303847
  EX_ac_e : 0.254923
  DM_5drib_c : 0.000099
  DM_4crsol_c : 0.000098

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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