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 : ppcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (39 of 117: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3399 b3831 b2744 b3708 b3008 b0871 b2883 b0121 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b0411 b4381 b2406 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b3821 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.775123 (mmol/gDw/h)
  Minimum Production Rate : 0.078818 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.518857
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.922993
  EX_pi_e : 0.984143
  EX_so4_e : 0.274010
  EX_k_e : 0.151299
  EX_fe2_e : 0.012449
  EX_mg2_e : 0.006724
  EX_cl_e : 0.004035
  EX_ca2_e : 0.004035
  EX_cu2_e : 0.000550
  EX_mn2_e : 0.000536
  EX_zn2_e : 0.000264
  EX_ni2_e : 0.000250
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.336612
  EX_co2_e : 26.291386
  EX_h_e : 7.358596
  Auxiliary production reaction : 0.078818
  DM_5drib_c : 0.000520
  DM_4crsol_c : 0.000173

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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