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 : btn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (60 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3399 b4382 b1241 b0351 b4069 b2744 b3708 b2297 b2458 b2883 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b3449 b0675 b2361 b0261 b0411 b0507 b4381 b2406 b0112 b0114 b2366 b2492 b0904 b1533 b0494 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.529320 (mmol/gDw/h)
  Minimum Production Rate : 0.259371 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 21.960211
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.065385
  EX_so4_e : 0.652035
  EX_pi_e : 0.510585
  EX_k_e : 0.103319
  EX_fe2_e : 0.008501
  EX_mg2_e : 0.004592
  EX_ca2_e : 0.002755
  EX_cl_e : 0.002755
  EX_cu2_e : 0.000375
  EX_mn2_e : 0.000366
  EX_zn2_e : 0.000180
  EX_ni2_e : 0.000171
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 43.040344
  EX_co2_e : 23.068067
  EX_h_e : 10.016328
  EX_ac_e : 3.048524
  DM_oxam_c : 0.533184
  DM_5drib_c : 0.259726
  EX_meoh_e : 0.259372
  DM_amob_c : 0.259372
  Auxiliary production reaction : 0.259371
  EX_glyclt_e : 0.000354
  DM_4crsol_c : 0.000118

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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