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 : prbatp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 47: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b4467 b4069 b4384 b2744 b3115 b1849 b2296 b2926 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b0207 b3012 b1982 b0261 b0411 b2799 b1602 b0153 b4381 b1727 b0114 b0529 b2492 b0904 b1781 b3001 b0591 b1380 b0325 b2660 b1771 b3662 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.410488 (mmol/gDw/h)
  Minimum Production Rate : 0.371904 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.864687
  EX_o2_e : 285.502581
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.295057
  EX_pi_e : 1.883576
  EX_so4_e : 0.103369
  EX_k_e : 0.080124
  EX_mg2_e : 0.003561
  EX_ca2_e : 0.002137
  EX_cl_e : 0.002137
  EX_cu2_e : 0.000291
  EX_mn2_e : 0.000284
  EX_zn2_e : 0.000140
  EX_ni2_e : 0.000133
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993407
  EX_h2o_e : 552.241028
  EX_co2_e : 35.996803
  EX_etoh_e : 0.547400
  Auxiliary production reaction : 0.371904
  EX_ac_e : 0.238981
  EX_ade_e : 0.000459
  DM_5drib_c : 0.000275
  DM_4crsol_c : 0.000092

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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