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 (113 of 120: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 60
  Gene deletion: b3553 b1478 b3399 b1241 b0351 b4069 b4384 b2744 b3708 b1479 b2297 b2458 b0160 b1238 b3236 b1779 b3962 b1982 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b1033 b2440 b3665 b0675 b2361 b1415 b1014 b4014 b0261 b2976 b2799 b3945 b3709 b1907 b4381 b2406 b3161 b0112 b3915 b0114 b0509 b3125 b1539 b2492 b0904 b3035 b1533 b1380 b1473 b0494 b4266 b2842 b1985 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.271311 (mmol/gDw/h)
  Minimum Production Rate : 0.319252 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.191043
  EX_o2_e : 283.545183
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.659028
  EX_so4_e : 0.560935
  EX_pi_e : 0.261708
  EX_k_e : 0.052958
  EX_mg2_e : 0.002354
  EX_ca2_e : 0.001412
  EX_cl_e : 0.001412
  EX_cu2_e : 0.000192
  EX_mn2_e : 0.000187
  EX_zn2_e : 0.000093
  EX_ni2_e : 0.000088

Product: (mmol/gDw/h)
  EX_fe3_e : 999.995642
  EX_h2o_e : 548.455056
  EX_co2_e : 34.557871
  EX_ac_e : 1.929337
  EX_met__L_e : 0.492614
  EX_dxylnt_e : 0.319433
  Auxiliary production reaction : 0.319252
  EX_ade_e : 0.000304
  DM_5drib_c : 0.000182
  DM_4crsol_c : 0.000061

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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