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 : 4ppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b2836 b3553 b0474 b2518 b3831 b4069 b4384 b3708 b3008 b3115 b1849 b2296 b2925 b2097 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b0651 b2162 b2690 b1982 b2797 b3117 b1814 b4471 b1033 b0261 b3945 b1602 b4381 b2406 b1727 b0114 b1539 b2492 b0904 b2578 b1533 b3927 b1380 b2660 b3662 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.372532 (mmol/gDw/h)
  Minimum Production Rate : 0.405861 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.548782
  EX_o2_e : 281.434485
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.565757
  EX_pi_e : 0.765207
  EX_so4_e : 0.093811
  EX_k_e : 0.072716
  EX_mg2_e : 0.003232
  EX_ca2_e : 0.001939
  EX_cl_e : 0.001939
  EX_cu2_e : 0.000264
  EX_mn2_e : 0.000257
  EX_zn2_e : 0.000127
  EX_ni2_e : 0.000120

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994017
  EX_h2o_e : 543.961583
  EX_co2_e : 32.568413
  EX_ac_e : 4.073958
  Auxiliary production reaction : 0.405861
  EX_thym_e : 0.067459
  EX_hxan_e : 0.000417
  DM_5drib_c : 0.000250
  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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