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 : ppcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (108 of 117: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 47
  Gene deletion: b4467 b1478 b1241 b4069 b4384 b3708 b3752 b3115 b1849 b2296 b2407 b3844 b1238 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b2797 b3117 b1814 b4471 b0261 b2799 b3945 b1602 b0153 b4381 b2406 b0452 b2975 b3603 b1539 b2492 b0904 b0591 b1533 b1380 b2660 b4141 b1798 b3662 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.396882 (mmol/gDw/h)
  Minimum Production Rate : 0.221132 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.114553
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.836433
  EX_pi_e : 1.046230
  EX_so4_e : 0.321074
  EX_k_e : 0.077469
  EX_fe2_e : 0.006374
  EX_mg2_e : 0.003443
  EX_ca2_e : 0.002066
  EX_cl_e : 0.002066
  EX_cu2_e : 0.000281
  EX_mn2_e : 0.000274
  EX_zn2_e : 0.000135
  EX_ni2_e : 0.000128

Product: (mmol/gDw/h)
  EX_h2o_e : 51.199811
  EX_co2_e : 36.292183
  EX_h_e : 5.366011
  EX_ac_e : 1.053687
  Auxiliary production reaction : 0.221132
  EX_ade_e : 0.000444
  DM_5drib_c : 0.000266
  DM_4crsol_c : 0.000089

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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