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 : dhpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (66 of 115: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b0871 b3617 b0030 b2407 b3236 b1982 b2210 b0261 b0507 b4381 b2406 b0112 b0511 b2975 b0114 b3603 b0529 b2492 b0904 b0515 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.376344 (mmol/gDw/h)
  Minimum Production Rate : 1.223403 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 22.732873
  EX_nh4_e : 11.406580
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.363023
  EX_so4_e : 0.094771
  EX_k_e : 0.073460
  EX_fe2_e : 0.006044
  EX_mg2_e : 0.003265
  EX_ca2_e : 0.001959
  EX_cl_e : 0.001959
  EX_cu2_e : 0.000267
  EX_mn2_e : 0.000260
  EX_zn2_e : 0.000128
  EX_ni2_e : 0.000122

Product: (mmol/gDw/h)
  EX_h2o_e : 51.381925
  EX_co2_e : 21.865497
  EX_h_e : 12.023499
  EX_acald_e : 2.778372
  Auxiliary production reaction : 1.223403
  EX_xan_e : 0.000421
  DM_5drib_c : 0.000253
  DM_4crsol_c : 0.000084

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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