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 : 2omph_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (41 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b0871 b2297 b2458 b2779 b2925 b2097 b0477 b3616 b3589 b3946 b0825 b4374 b2361 b2291 b2913 b0114 b2492 b0904 b0515 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.341781 (mmol/gDw/h)
  Minimum Production Rate : 0.104293 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.076774
  EX_glc__D_e : 10.000000
  EX_nh4_e : 3.691209
  EX_pi_e : 0.329684
  EX_so4_e : 0.086067
  EX_k_e : 0.066713
  EX_fe2_e : 0.005489
  EX_mg2_e : 0.002965
  EX_ca2_e : 0.001779
  EX_cl_e : 0.001779
  EX_cu2_e : 0.000242
  EX_mn2_e : 0.000236
  EX_zn2_e : 0.000117
  EX_ni2_e : 0.000110

Product: (mmol/gDw/h)
  EX_h2o_e : 43.342906
  EX_co2_e : 29.987958
  EX_h_e : 7.090108
  EX_pyr_e : 3.182224
  EX_ac_e : 0.767348
  Auxiliary production reaction : 0.104293
  EX_glyc__R_e : 0.000114
  DM_5drib_c : 0.000077
  DM_4crsol_c : 0.000076

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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