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 : pnto__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (44 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b2836 b3399 b2744 b3708 b3008 b0871 b3115 b1849 b2296 b2925 b2097 b0160 b2690 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b0822 b4381 b2406 b1727 b0114 b2366 b2492 b0904 b2578 b1533 b3927 b2413 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.518913 (mmol/gDw/h)
  Minimum Production Rate : 0.316467 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.955669
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.934837
  EX_pi_e : 0.500546
  EX_so4_e : 0.130673
  EX_k_e : 0.101288
  EX_fe2_e : 0.008334
  EX_mg2_e : 0.004502
  EX_ca2_e : 0.002701
  EX_cl_e : 0.002701
  EX_cu2_e : 0.000368
  EX_mn2_e : 0.000359
  EX_zn2_e : 0.000177
  EX_ni2_e : 0.000168
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 45.015674
  EX_co2_e : 28.065392
  EX_h_e : 8.015211
  EX_pyr_e : 2.585984
  Auxiliary production reaction : 0.316467
  DM_oxam_c : 0.014159
  DM_5drib_c : 0.000348
  DM_4crsol_c : 0.000116

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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