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 : hpyr_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4467 b3399 b4069 b2744 b3115 b1849 b2296 b2925 b2097 b1004 b3713 b1109 b0046 b3124 b3236 b1779 b3946 b0825 b1602 b4381 b2789 b3127 b1727 b2975 b0114 b3603 b0529 b2492 b0904 b1380 b2660 b0514 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.398625 (mmol/gDw/h)
  Minimum Production Rate : 0.013672 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.607316
  EX_o2_e : 282.191171
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.873301
  EX_pi_e : 0.384516
  EX_so4_e : 0.100382
  EX_k_e : 0.077809
  EX_mg2_e : 0.003458
  EX_ca2_e : 0.002075
  EX_cl_e : 0.002075
  EX_cu2_e : 0.000283
  EX_mn2_e : 0.000275
  EX_zn2_e : 0.000136
  EX_ni2_e : 0.000129

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993598
  EX_h2o_e : 544.419104
  EX_co2_e : 32.745680
  EX_ac_e : 5.141699
  EX_ade_e : 0.113637
  Auxiliary production reaction : 0.013672
  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.

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Last updated: 21-Sep-2023
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