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 : duri_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (44 of 50: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b4382 b1241 b0351 b4384 b3708 b3008 b0871 b2297 b2458 b2925 b2097 b3617 b0030 b2407 b1779 b2797 b3117 b1814 b4471 b3946 b0825 b3665 b2406 b0112 b3654 b3714 b3664 b0114 b2366 b0529 b2492 b0904 b2947 b1533 b3927 b3821 b2413 b3662 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.348376 (mmol/gDw/h)
  Minimum Production Rate : 0.241219 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.083523
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.244869
  EX_pi_e : 0.336045
  EX_so4_e : 0.087728
  EX_k_e : 0.068001
  EX_fe2_e : 0.005595
  EX_mg2_e : 0.003022
  EX_ca2_e : 0.001813
  EX_cl_e : 0.001813
  EX_cu2_e : 0.000247
  EX_mn2_e : 0.000241
  EX_zn2_e : 0.000119
  EX_ni2_e : 0.000113

Product: (mmol/gDw/h)
  EX_h2o_e : 43.821359
  EX_co2_e : 27.997091
  EX_h_e : 8.860764
  EX_pyr_e : 5.177309
  Auxiliary production reaction : 0.241219
  EX_mththf_e : 0.000156
  DM_5drib_c : 0.000078
  DM_4crsol_c : 0.000078

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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