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 : fpram_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (39 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b2836 b1241 b0351 b4384 b2744 b3708 b3008 b0871 b3115 b1849 b2296 b2407 b1779 b2688 b2797 b3117 b1814 b4471 b3616 b3589 b4381 b2406 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b2366 b0529 b2492 b0904 b2578 b1533 b3927 b3662 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.476347 (mmol/gDw/h)
  Minimum Production Rate : 0.164881 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.285769
  EX_o2_e : 288.274633
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.639075
  EX_pi_e : 0.624343
  EX_so4_e : 0.119955
  EX_k_e : 0.092980
  EX_mg2_e : 0.004132
  EX_cl_e : 0.002479
  EX_ca2_e : 0.002479
  EX_cu2_e : 0.000338
  EX_mn2_e : 0.000329
  EX_zn2_e : 0.000162
  EX_ni2_e : 0.000154
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992347
  EX_h2o_e : 552.692545
  EX_co2_e : 39.128228
  Auxiliary production reaction : 0.164855
  DM_mththf_c : 0.000213
  DM_5drib_c : 0.000107
  DM_4crsol_c : 0.000106

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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