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 : adp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (84 of 89: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b4467 b4382 b4069 b4384 b3708 b2297 b2458 b2926 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1982 b2797 b3117 b1814 b4471 b0261 b1602 b2913 b2406 b3915 b1727 b0114 b1539 b2492 b0904 b1533 b2835 b1380 b0494 b1771 b3662 b0606 b0221 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.468819 (mmol/gDw/h)
  Minimum Production Rate : 0.198800 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.140771
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.058469
  EX_pi_e : 0.849825
  EX_so4_e : 0.118058
  EX_k_e : 0.091510
  EX_fe3_e : 0.007530
  EX_mg2_e : 0.004067
  EX_ca2_e : 0.002440
  EX_cl_e : 0.002440
  EX_cu2_e : 0.000332
  EX_mn2_e : 0.000324
  EX_zn2_e : 0.000160
  EX_ni2_e : 0.000151
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.609027
  EX_co2_e : 37.645335
  EX_h_e : 5.576740
  EX_ac_e : 0.272940
  Auxiliary production reaction : 0.198800
  EX_3hpp_e : 0.192111
  EX_hxan_e : 0.000316
  DM_5drib_c : 0.000105
  DM_4crsol_c : 0.000105

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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