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 : 4c2me_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (95 of 96: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b4467 b2242 b2744 b1278 b3614 b0910 b0871 b2779 b2925 b2097 b2781 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1759 b3946 b0825 b4374 b0675 b1415 b4015 b1602 b4138 b4123 b0621 b2913 b4381 b0114 b0529 b2492 b0904 b3028 b1380 b3918 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.346184 (mmol/gDw/h)
  Minimum Production Rate : 0.043268 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.852255
  EX_o2_e : 279.740987
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.273022
  EX_pi_e : 0.420468
  EX_so4_e : 0.087176
  EX_k_e : 0.067573
  EX_mg2_e : 0.003003
  EX_cl_e : 0.001802
  EX_ca2_e : 0.001802
  EX_cu2_e : 0.000245
  EX_mn2_e : 0.000239
  EX_zn2_e : 0.000118
  EX_ni2_e : 0.000112

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994440
  EX_h2o_e : 543.550906
  EX_co2_e : 27.719442
  EX_pyr_e : 4.791352
  EX_succ_e : 0.360998
  EX_thymd_e : 0.139567
  EX_ura_e : 0.062660
  Auxiliary production reaction : 0.043268
  EX_dxylnt_e : 0.000232
  DM_5drib_c : 0.000078
  DM_4crsol_c : 0.000077

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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