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 : dpcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b4069 b4384 b2744 b3708 b3008 b2297 b2458 b0030 b2407 b1779 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b0261 b1701 b1805 b4381 b2406 b0114 b1539 b2492 b0904 b3035 b2578 b1533 b3927 b3447 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.643557 (mmol/gDw/h)
  Minimum Production Rate : 0.162490 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.535793
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.087794
  EX_pi_e : 0.945759
  EX_so4_e : 0.324551
  EX_k_e : 0.125618
  EX_fe2_e : 0.010336
  EX_mg2_e : 0.005583
  EX_cl_e : 0.003350
  EX_ca2_e : 0.003350
  EX_cu2_e : 0.000456
  EX_mn2_e : 0.000445
  EX_zn2_e : 0.000219
  EX_ni2_e : 0.000208
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 49.000142
  EX_co2_e : 29.075376
  EX_h_e : 6.937891
  EX_ac_e : 0.537160
  Auxiliary production reaction : 0.162490
  DM_5drib_c : 0.002224
  DM_4crsol_c : 0.001936

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.

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Last updated: 21-Sep-2023
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