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 : ins_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (20 of 37: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b2836 b4382 b4384 b3708 b3008 b0871 b2925 b2097 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b0261 b0411 b2406 b0114 b1539 b2492 b0904 b1533 b3927   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.775260 (mmol/gDw/h)
  Minimum Production Rate : 0.095926 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.232829
  EX_o2_e : 274.693353
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.003196
  EX_pi_e : 0.747820
  EX_so4_e : 0.195226
  EX_k_e : 0.151325
  EX_mg2_e : 0.006725
  EX_ca2_e : 0.004035
  EX_cl_e : 0.004035
  EX_cu2_e : 0.000550
  EX_mn2_e : 0.000536
  EX_zn2_e : 0.000264
  EX_ni2_e : 0.000250
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_fe3_e : 999.987549
  EX_h2o_e : 547.906008
  EX_co2_e : 25.987002
  EX_acser_e : 0.245883
  Auxiliary production reaction : 0.095926
  DM_oxam_c : 0.000868
  DM_5drib_c : 0.000520
  DM_4crsol_c : 0.000173

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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