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 : quln_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (101 of 106: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4467 b2242 b2930 b4232 b3697 b3925 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b3946 b0825 b1415 b4015 b4138 b4123 b0621 b2913 b0114 b0755 b3612 b2492 b0904 b3028 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.400641 (mmol/gDw/h)
  Minimum Production Rate : 0.284114 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 31.675190
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.611007
  EX_pi_e : 0.386461
  EX_so4_e : 0.100890
  EX_k_e : 0.078202
  EX_fe2_e : 0.006435
  EX_mg2_e : 0.003476
  EX_ca2_e : 0.002085
  EX_cl_e : 0.002085
  EX_cu2_e : 0.000284
  EX_mn2_e : 0.000277
  EX_zn2_e : 0.000137
  EX_ni2_e : 0.000129
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 44.597269
  EX_co2_e : 31.894969
  EX_h_e : 9.369066
  EX_ac_e : 3.999632
  EX_succ_e : 0.417786
  Auxiliary production reaction : 0.284114
  EX_dxylnt_e : 0.000268
  DM_5drib_c : 0.000090
  DM_4crsol_c : 0.000089

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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