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 : dcmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (107 of 117: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b2836 b3399 b4069 b4384 b2744 b3708 b3008 b3752 b0512 b0871 b3115 b1849 b2296 b2925 b2097 b1238 b2883 b1779 b2690 b1982 b2797 b3117 b1814 b4471 b1623 b0261 b0411 b3945 b0507 b4381 b2406 b0112 b2975 b0114 b3603 b0529 b1539 b2492 b0904 b0591 b2578 b1533 b3927 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.572640 (mmol/gDw/h)
  Minimum Production Rate : 0.727568 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 26.090554
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.369729
  EX_pi_e : 1.279940
  EX_so4_e : 0.144202
  EX_k_e : 0.111775
  EX_fe2_e : 0.009197
  EX_mg2_e : 0.004968
  EX_ca2_e : 0.002981
  EX_cl_e : 0.002981
  EX_cu2_e : 0.000406
  EX_mn2_e : 0.000396
  EX_zn2_e : 0.000195
  EX_ni2_e : 0.000185
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 48.068848
  EX_co2_e : 26.044452
  EX_h_e : 8.857825
  EX_pyr_e : 1.077531
  Auxiliary production reaction : 0.727568
  EX_ac_e : 0.333383
  EX_alltn_e : 0.000641
  DM_5drib_c : 0.000384
  DM_4crsol_c : 0.000128

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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