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 : dgtp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b0474 b2518 b1241 b0351 b4069 b4384 b3708 b0871 b3115 b1849 b2296 b2779 b2925 b2097 b3617 b0030 b2407 b0907 b2690 b2797 b3117 b1814 b4471 b0261 b3945 b4381 b2868 b0114 b1539 b2492 b0904 b1533 b1813   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.551343 (mmol/gDw/h)
  Minimum Production Rate : 0.550107 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.523143
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.706846
  EX_pi_e : 2.182148
  EX_so4_e : 0.138839
  EX_k_e : 0.107618
  EX_fe2_e : 0.008855
  EX_mg2_e : 0.004783
  EX_ca2_e : 0.002870
  EX_cl_e : 0.002870
  EX_cu2_e : 0.000391
  EX_mn2_e : 0.000381
  EX_zn2_e : 0.000188
  EX_ni2_e : 0.000178
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 48.968828
  EX_co2_e : 25.942749
  EX_h_e : 9.299473
  EX_ac_e : 1.819785
  EX_pyr_e : 0.761431
  Auxiliary production reaction : 0.550107
  EX_ade_e : 0.000371
  DM_5drib_c : 0.000124
  DM_4crsol_c : 0.000123
  EX_glyc__R_e : 0.000123

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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