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 : glyclt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (20 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b2297 b2458 b3617 b2883 b1982 b0675 b2361 b2291 b0261 b0411 b0507 b4381 b0112 b2975 b0114 b3603 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.513816 (mmol/gDw/h)
  Minimum Production Rate : 0.505582 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 20.021099
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.971850
  EX_pi_e : 0.495630
  EX_so4_e : 0.129389
  EX_k_e : 0.100293
  EX_fe2_e : 0.008252
  EX_mg2_e : 0.004457
  EX_ca2_e : 0.002674
  EX_cl_e : 0.002674
  EX_cu2_e : 0.000364
  EX_mn2_e : 0.000355
  EX_zn2_e : 0.000175
  EX_ni2_e : 0.000166
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 42.484805
  EX_co2_e : 20.637712
  EX_h_e : 8.454702
  EX_thymd_e : 0.958264
  DM_oxam_c : 0.506157
  DM_5drib_c : 0.505927
  DM_4crsol_c : 0.505696
  Auxiliary production reaction : 0.505582
  EX_ac_e : 0.299136

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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