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 (73 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b4467 b1478 b1241 b4069 b3708 b2930 b4232 b3697 b3925 b3115 b1849 b2296 b1238 b1004 b3713 b1109 b0046 b3236 b1779 b2797 b3117 b1814 b4471 b3946 b0825 b4015 b0261 b2799 b3945 b1602 b2913 b4381 b2406 b3915 b3654 b3714 b3664 b4064 b4464 b1539 b2492 b0904 b1533 b1380 b0606 b0221 b2285 b1011 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.373275 (mmol/gDw/h)
  Minimum Production Rate : 0.538820 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.969740
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.570104
  EX_pi_e : 0.360064
  EX_so4_e : 0.093999
  EX_k_e : 0.072861
  EX_fe3_e : 0.005997
  EX_mg2_e : 0.003238
  EX_ca2_e : 0.001943
  EX_cl_e : 0.001943
  EX_cu2_e : 0.000265
  EX_mn2_e : 0.000258
  EX_zn2_e : 0.000127
  EX_ni2_e : 0.000121

Product: (mmol/gDw/h)
  EX_h2o_e : 43.238276
  EX_co2_e : 32.306580
  EX_h_e : 8.274984
  EX_ac_e : 3.761660
  Auxiliary production reaction : 0.538763
  DM_5drib_c : 0.000084
  DM_4crsol_c : 0.000083

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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