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 : gdptp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (48 of 70: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b1241 b0351 b4069 b4384 b3708 b2297 b2458 b3617 b0030 b2407 b1238 b1779 b1982 b2797 b3117 b1814 b4471 b0261 b4381 b2406 b0112 b0114 b2366 b2492 b0904 b1533 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.531304 (mmol/gDw/h)
  Minimum Production Rate : 0.794931 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.455631
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.712691
  EX_pi_e : 4.487155
  EX_so4_e : 0.133793
  EX_k_e : 0.103707
  EX_fe2_e : 0.008533
  EX_mg2_e : 0.004609
  EX_cl_e : 0.002765
  EX_ca2_e : 0.002765
  EX_cu2_e : 0.000377
  EX_mn2_e : 0.000367
  EX_zn2_e : 0.000181
  EX_ni2_e : 0.000172
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 52.953930
  EX_co2_e : 26.204768
  EX_h_e : 8.490272
  EX_ac_e : 2.018579
  Auxiliary production reaction : 0.794931
  DM_5drib_c : 0.000357
  DM_4crsol_c : 0.000118

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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