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 : dump_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (60 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b4467 b1478 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b4384 b3752 b0871 b2779 b2407 b1004 b3713 b1109 b0046 b3236 b0207 b3012 b1982 b0261 b0411 b2799 b1602 b2913 b3915 b0452 b0529 b2492 b0904 b1781 b3001 b1380 b0325 b1771 b0606 b2285 b1011 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.386228 (mmol/gDw/h)
  Minimum Production Rate : 1.046235 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.949443
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.265426
  EX_pi_e : 1.418792
  EX_so4_e : 0.097261
  EX_k_e : 0.075389
  EX_fe3_e : 0.006205
  EX_mg2_e : 0.003351
  EX_ca2_e : 0.002010
  EX_cl_e : 0.002010
  EX_cu2_e : 0.000274
  EX_mn2_e : 0.000267
  EX_zn2_e : 0.000132
  EX_ni2_e : 0.000125

Product: (mmol/gDw/h)
  EX_h2o_e : 52.251625
  EX_co2_e : 34.727987
  EX_h_e : 5.649219
  Auxiliary production reaction : 1.046234
  EX_hxan_e : 0.000432
  DM_5drib_c : 0.000259
  DM_4crsol_c : 0.000086

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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