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 : 5mthf_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (96 of 120: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b4467 b1478 b1241 b4069 b4384 b3708 b2297 b2458 b2779 b0030 b2407 b3844 b1238 b1004 b3713 b1109 b0046 b3236 b0207 b3012 b0937 b1982 b2797 b3117 b1814 b4471 b0261 b2799 b1602 b4381 b2406 b2366 b2492 b0904 b1781 b3001 b1533 b3821 b1380 b0325 b2660 b1771 b4141 b1798 b3662 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.435903 (mmol/gDw/h)
  Minimum Production Rate : 0.221039 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.689430
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.256936
  EX_pi_e : 0.420474
  EX_so4_e : 0.109769
  EX_k_e : 0.085085
  EX_fe2_e : 0.007001
  EX_mg2_e : 0.003781
  EX_ca2_e : 0.002269
  EX_cl_e : 0.002269
  EX_cu2_e : 0.000309
  EX_mn2_e : 0.000301
  EX_zn2_e : 0.000149
  EX_ni2_e : 0.000141
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.670531
  EX_co2_e : 37.176455
  EX_h_e : 6.029287
  EX_ac_e : 0.253776
  Auxiliary production reaction : 0.221039
  EX_hxan_e : 0.000488
  DM_5drib_c : 0.000292
  DM_4crsol_c : 0.000097

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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