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 : 5mthf_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (106 of 120: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 57
  Gene deletion: b2836 b3553 b1478 b4382 b1241 b0351 b4069 b4384 b3708 b1479 b3752 b3115 b1849 b2296 b2407 b3236 b1779 b3962 b1982 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b1033 b0596 b1415 b1014 b4014 b0261 b2976 b2799 b3945 b3709 b1907 b2406 b3161 b0112 b3915 b2868 b4265 b0114 b0509 b3125 b1539 b2492 b0904 b1533 b1380 b1473 b4266 b3662 b1985 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.248996 (mmol/gDw/h)
  Minimum Production Rate : 0.527824 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.669181
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.602429
  EX_so4_e : 0.279850
  EX_pi_e : 0.240183
  EX_k_e : 0.048602
  EX_fe3_e : 0.004000
  EX_mg2_e : 0.002160
  EX_ca2_e : 0.001296
  EX_cl_e : 0.001296
  EX_cu2_e : 0.000177
  EX_mn2_e : 0.000172
  EX_zn2_e : 0.000085
  EX_ni2_e : 0.000080

Product: (mmol/gDw/h)
  EX_h2o_e : 48.935307
  EX_co2_e : 32.424136
  EX_h_e : 8.362510
  EX_ac_e : 1.535828
  EX_dxylnt_e : 0.527988
  Auxiliary production reaction : 0.527821
  EX_met__L_e : 0.217147
  EX_ade_e : 0.000279
  DM_5drib_c : 0.000167
  DM_4crsol_c : 0.000056

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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