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 : ps120_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (69 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b2836 b3831 b2744 b3614 b0910 b3752 b4152 b2781 b3844 b1612 b1611 b4122 b1759 b4374 b2361 b2291 b4388 b4138 b4123 b0621 b2406 b3453 b2197 b3918 b1912 b2240 b1206 b1378   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.615176 (mmol/gDw/h)
  Minimum Production Rate : 0.031643 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 994.145700
  EX_h_e : 986.327838
  EX_o2_e : 276.343003
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.547990
  EX_pi_e : 0.918304
  EX_so4_e : 0.154914
  EX_k_e : 0.120078
  EX_mg2_e : 0.005337
  EX_ca2_e : 0.003202
  EX_cl_e : 0.003202
  EX_cu2_e : 0.000436
  EX_mn2_e : 0.000425
  EX_zn2_e : 0.000210
  EX_ni2_e : 0.000199
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 994.135819
  EX_h2o_e : 544.872109
  EX_co2_e : 28.609783
  EX_succ_e : 0.641500
  EX_ura_e : 0.436251
  EX_glyc3p_e : 0.293259
  Auxiliary production reaction : 0.031643
  DM_5drib_c : 0.000138
  DM_4crsol_c : 0.000137

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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