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 : amet_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (83 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 50
  Gene deletion: b3553 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b3831 b4384 b3708 b3008 b3614 b0910 b3752 b0871 b3115 b1849 b2296 b2407 b3236 b1779 b3962 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b1033 b3665 b1415 b1014 b3945 b4381 b2406 b0112 b0114 b2366 b2492 b0904 b1533 b1380 b0325 b2413 b4266 b3662 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.407679 (mmol/gDw/h)
  Minimum Production Rate : 0.101125 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 996.047253
  EX_o2_e : 285.796845
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.411091
  EX_so4_e : 0.456174
  EX_pi_e : 0.393250
  EX_k_e : 0.079576
  EX_mg2_e : 0.003537
  EX_ca2_e : 0.002122
  EX_cl_e : 0.002122
  EX_cu2_e : 0.000289
  EX_mn2_e : 0.000282
  EX_zn2_e : 0.000139
  EX_ni2_e : 0.000132
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993452
  EX_h2o_e : 550.857648
  EX_co2_e : 37.802852
  EX_acald_e : 1.156071
  EX_met__L_e : 0.252387
  Auxiliary production reaction : 0.101125
  EX_thym_e : 0.073824
  EX_ade_e : 0.000274
  EX_dxylnt_e : 0.000273
  DM_mththf_c : 0.000183
  DM_5drib_c : 0.000092
  DM_4crsol_c : 0.000091
  EX_etha_e : 0.000033

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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