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 : btn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b4467 b1478 b4382 b1241 b0351 b4069 b4384 b3708 b3752 b3115 b1849 b2296 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b2797 b3117 b1814 b4471 b0261 b0411 b0335 b2799 b3945 b1602 b0153 b2913 b4381 b2406 b0452 b4064 b4464 b2975 b3603 b0584 b0728 b2366 b2492 b0904 b1533 b1380 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.361630 (mmol/gDw/h)
  Minimum Production Rate : 0.099484 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 35.895020
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.147818
  EX_pi_e : 0.348830
  EX_so4_e : 0.290034
  EX_k_e : 0.070588
  EX_fe2_e : 0.005808
  EX_mg2_e : 0.003137
  EX_ca2_e : 0.001882
  EX_cl_e : 0.001882
  EX_cu2_e : 0.000256
  EX_mn2_e : 0.000250
  EX_zn2_e : 0.000123
  EX_ni2_e : 0.000117

Product: (mmol/gDw/h)
  EX_h2o_e : 52.223908
  EX_co2_e : 35.305101
  EX_h_e : 8.183460
  EX_ac_e : 1.916867
  EX_xan_e : 0.387249
  EX_ade_e : 0.199373
  DM_5drib_c : 0.099727
  EX_meoh_e : 0.099485
  DM_amob_c : 0.099485
  Auxiliary production reaction : 0.099484
  DM_4crsol_c : 0.000081

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.

Last updated: 21-Sep-2023
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