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 : bmoco1gdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (136 of 137: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 55
  Gene deletion: b3553 b1478 b1241 b4069 b4384 b2744 b3708 b0910 b3752 b3115 b1849 b2296 b2779 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b2920 b1982 b0477 b4139 b2797 b3117 b1814 b4471 b1033 b4374 b2361 b2291 b0261 b2799 b3945 b1602 b2406 b3915 b0728 b0509 b3125 b1539 b2492 b0904 b2954 b1298 b1533 b3825 b3029 b1380 b2660 b3662 b0221 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.464041 (mmol/gDw/h)
  Minimum Production Rate : 0.042648 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.840499
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.653868
  EX_pi_e : 0.575550
  EX_so4_e : 0.287433
  EX_k_e : 0.090578
  EX_mobd_e : 0.042647
  EX_fe3_e : 0.007455
  EX_mg2_e : 0.004026
  EX_ca2_e : 0.002415
  EX_cl_e : 0.002415
  EX_cu2_e : 0.000329
  EX_mn2_e : 0.000321
  EX_zn2_e : 0.000158
  EX_ni2_e : 0.000150
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.920662
  EX_co2_e : 38.788800
  EX_h_e : 4.842518
  EX_ac_e : 0.440736
  Auxiliary production reaction : 0.042644
  EX_ade_e : 0.000519
  DM_5drib_c : 0.000311
  DM_4crsol_c : 0.000103

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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