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 : ametam_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (76 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b2836 b3553 b3399 b4069 b2744 b3708 b3115 b1849 b2296 b2925 b2097 b0160 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b1033 b4374 b0675 b2361 b2291 b0261 b3945 b1602 b1727 b0114 b2366 b2492 b0904 b1533 b3927 b1380 b2660 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.380698 (mmol/gDw/h)
  Minimum Production Rate : 0.096758 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.662092
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.693754
  EX_fe3_e : 0.501108
  EX_pi_e : 0.367223
  EX_so4_e : 0.192625
  EX_k_e : 0.074310
  EX_mg2_e : 0.003303
  EX_ca2_e : 0.001982
  EX_cl_e : 0.001982
  EX_cu2_e : 0.000270
  EX_mn2_e : 0.000263
  EX_zn2_e : 0.000130
  EX_ni2_e : 0.000123

Product: (mmol/gDw/h)
  EX_h2o_e : 43.759871
  EX_co2_e : 32.695563
  EX_h_e : 9.354807
  EX_ac_e : 5.160476
  EX_fe2_e : 0.494993
  Auxiliary production reaction : 0.096758
  EX_hxan_e : 0.000426
  DM_5drib_c : 0.000255
  DM_4crsol_c : 0.000085

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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