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 : aps_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4467 b4069 b4384 b3752 b3115 b1849 b2296 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b3665 b0411 b1602 b0153 b4381 b3654 b3714 b3664 b1727 b0114 b0529 b2492 b0904 b3035 b1380 b2660 b1771 b1517 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.438942 (mmol/gDw/h)
  Minimum Production Rate : 0.203125 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.108674
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.756161
  EX_pi_e : 0.626531
  EX_so4_e : 0.313660
  EX_k_e : 0.085678
  EX_fe2_e : 0.007050
  EX_mg2_e : 0.003808
  EX_ca2_e : 0.002285
  EX_cl_e : 0.002285
  EX_cu2_e : 0.000311
  EX_mn2_e : 0.000303
  EX_zn2_e : 0.000150
  EX_ni2_e : 0.000142
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 49.769440
  EX_co2_e : 36.513211
  EX_h_e : 4.898094
  EX_12ppd__R_e : 0.975639
  EX_ac_e : 0.255546
  Auxiliary production reaction : 0.203125
  EX_mththf_e : 0.000197
  DM_5drib_c : 0.000099
  DM_4crsol_c : 0.000098

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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