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 : preq1_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (72 of 95: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3553 b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b0871 b3617 b0030 b2883 b1982 b1033 b1623 b0261 b0411 b0507 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 : 0.470913 (mmol/gDw/h)
  Minimum Production Rate : 1.506181 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.529165
  EX_nh4_e : 12.629573
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.454245
  EX_so4_e : 0.118585
  EX_k_e : 0.091919
  EX_fe2_e : 0.007563
  EX_mg2_e : 0.004085
  EX_ca2_e : 0.002451
  EX_cl_e : 0.002451
  EX_cu2_e : 0.000334
  EX_mn2_e : 0.000325
  EX_zn2_e : 0.000161
  EX_ni2_e : 0.000152
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 50.745055
  EX_co2_e : 23.222041
  EX_h_e : 10.377672
  EX_acald_e : 3.439253
  Auxiliary production reaction : 1.506181
  DM_oxam_c : 0.012849
  DM_5drib_c : 0.000316
  EX_glyclt_e : 0.000315
  DM_4crsol_c : 0.000105

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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