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 : succoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (26 of 28: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 54
  Gene deletion: b4467 b2836 b1478 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b4384 b3708 b3008 b2930 b4232 b3697 b3925 b0871 b2779 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b2690 b1982 b2797 b3117 b1814 b4471 b4015 b0261 b0411 b2799 b3945 b1602 b2223 b2406 b3915 b2366 b2492 b0904 b1533 b1380 b1600 b2660 b4141 b1798 b0606 b2285 b1011 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.343099 (mmol/gDw/h)
  Minimum Production Rate : 0.093033 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 29.658541
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.358546
  EX_pi_e : 0.610037
  EX_so4_e : 0.179427
  EX_k_e : 0.066970
  EX_fe3_e : 0.005512
  EX_mg2_e : 0.002976
  EX_ca2_e : 0.001786
  EX_cl_e : 0.001786
  EX_cu2_e : 0.000243
  EX_mn2_e : 0.000237
  EX_zn2_e : 0.000117
  EX_ni2_e : 0.000111

Product: (mmol/gDw/h)
  EX_h2o_e : 44.082927
  EX_co2_e : 33.067986
  EX_acald_e : 5.260514
  EX_h_e : 3.532067
  Auxiliary production reaction : 0.093027
  EX_ade_e : 0.000384
  DM_5drib_c : 0.000230
  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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