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 : pe161_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4467 b1054 b2836 b2242 b4382 b3831 b4384 b3614 b0910 b3752 b2781 b3844 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1759 b1415 b4014 b2976 b4138 b4123 b0621 b0153 b2223 b0590 b2406 b2492 b0904 b2197 b3028 b3918 b1912 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.458684 (mmol/gDw/h)
  Minimum Production Rate : 0.242215 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 25.354050
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.846514
  EX_pi_e : 0.684664
  EX_so4_e : 0.115506
  EX_k_e : 0.089532
  EX_fe2_e : 0.007367
  EX_mg2_e : 0.003979
  EX_ca2_e : 0.002387
  EX_cl_e : 0.002387
  EX_cu2_e : 0.000325
  EX_mn2_e : 0.000317
  EX_zn2_e : 0.000156
  EX_ni2_e : 0.000148
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 44.425169
  EX_co2_e : 28.996829
  EX_h_e : 5.579532
  EX_succ_e : 0.478312
  EX_ura_e : 0.325275
  Auxiliary production reaction : 0.242215
  DM_5drib_c : 0.000103
  DM_4crsol_c : 0.000102

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.

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Last updated: 21-Sep-2023
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