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 : hpyr_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (35 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3752 b0871 b2779 b2926 b3617 b2407 b1982 b0261 b2913 b4381 b2406 b0112 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.445824 (mmol/gDw/h)
  Minimum Production Rate : 0.362466 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.976286
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.539997
  EX_pi_e : 0.430045
  EX_so4_e : 0.112267
  EX_k_e : 0.087022
  EX_fe2_e : 0.007160
  EX_mg2_e : 0.003868
  EX_ca2_e : 0.002321
  EX_cl_e : 0.002321
  EX_cu2_e : 0.000316
  EX_mn2_e : 0.000308
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 42.594469
  EX_co2_e : 26.834847
  EX_h_e : 5.909144
  EX_acald_e : 1.815923
  DM_oxam_c : 0.725133
  DM_5drib_c : 0.724933
  DM_4crsol_c : 0.724734
  Auxiliary production reaction : 0.362466

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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