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 : prpncoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (35 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3399 b2744 b3708 b3008 b0871 b2883 b2797 b3117 b1814 b4471 b2440 b1623 b3665 b0261 b0411 b4381 b2406 b0452 b3654 b3714 b3664 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.770560 (mmol/gDw/h)
  Minimum Production Rate : 0.078765 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.758402
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.873394
  EX_pi_e : 0.979580
  EX_so4_e : 0.272807
  EX_k_e : 0.150408
  EX_fe2_e : 0.012376
  EX_mg2_e : 0.006685
  EX_ca2_e : 0.004011
  EX_cl_e : 0.004011
  EX_cu2_e : 0.000546
  EX_mn2_e : 0.000532
  EX_zn2_e : 0.000263
  EX_ni2_e : 0.000249
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.483996
  EX_co2_e : 26.481588
  EX_h_e : 7.316504
  Auxiliary production reaction : 0.078765
  DM_5drib_c : 0.000173
  DM_4crsol_c : 0.000172
  EX_etha_e : 0.000062

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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