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 : adn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (78 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4467 b4069 b4384 b3708 b3115 b1849 b2296 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b1982 b4139 b2797 b3117 b1814 b4471 b2440 b3665 b0411 b1602 b2913 b4381 b1727 b0114 b2366 b2492 b0904 b1533 b3029 b1380 b1517 b0221 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.482945 (mmol/gDw/h)
  Minimum Production Rate : 0.047842 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.634342
  EX_o2_e : 287.533305
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.891336
  EX_pi_e : 0.465852
  EX_so4_e : 0.121615
  EX_k_e : 0.094267
  EX_mg2_e : 0.004190
  EX_ca2_e : 0.002514
  EX_cl_e : 0.002514
  EX_cu2_e : 0.000342
  EX_mn2_e : 0.000334
  EX_zn2_e : 0.000165
  EX_ni2_e : 0.000156
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992243
  EX_h2o_e : 551.941687
  EX_co2_e : 38.264398
  EX_gly_e : 0.398411
  EX_ac_e : 0.281164
  Auxiliary production reaction : 0.047842
  EX_etha_e : 0.036324
  EX_ade_e : 0.000325
  EX_mththf_e : 0.000216
  DM_5drib_c : 0.000109
  DM_4crsol_c : 0.000108

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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