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 : ser__D_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (85 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 50
  Gene deletion: b4467 b2836 b1478 b3399 b1241 b4069 b2744 b3708 b2297 b2458 b0160 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b3908 b1656 b0207 b3012 b1982 b4139 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b4015 b0261 b2799 b1602 b2913 b3915 b2366 b2492 b0904 b2954 b1781 b3001 b1533 b1380 b0325 b1771 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.493665 (mmol/gDw/h)
  Minimum Production Rate : 0.305905 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.340213
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.637450
  EX_pi_e : 0.476193
  EX_so4_e : 0.124315
  EX_k_e : 0.096360
  EX_fe3_e : 0.007929
  EX_mg2_e : 0.004283
  EX_ca2_e : 0.002570
  EX_cl_e : 0.002570
  EX_cu2_e : 0.000350
  EX_mn2_e : 0.000341
  EX_zn2_e : 0.000168
  EX_ni2_e : 0.000159
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 51.580850
  EX_co2_e : 38.242569
  EX_h_e : 5.137787
  Auxiliary production reaction : 0.305905
  EX_ac_e : 0.287405
  EX_glyclt_e : 0.000552
  DM_5drib_c : 0.000331
  DM_4crsol_c : 0.000110

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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