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 (94 of 120: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b2836 b3553 b3399 b1241 b0351 b4069 b2502 b2744 b3708 b3115 b1849 b2296 b2926 b3124 b0907 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b1033 b4374 b0675 b2361 b2291 b4014 b0261 b2976 b3709 b3161 b0112 b2789 b3127 b3915 b0114 b0755 b3612 b1539 b2492 b0904 b0591 b1533 b1473 b4141 b1798 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.316052 (mmol/gDw/h)
  Minimum Production Rate : 0.945592 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 986.905863
  EX_o2_e : 274.563834
  EX_nh4_e : 10.032831
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.304866
  EX_so4_e : 0.079588
  EX_k_e : 0.061691
  EX_mg2_e : 0.002742
  EX_ca2_e : 0.001645
  EX_cl_e : 0.001645
  EX_cu2_e : 0.000224
  EX_mn2_e : 0.000218
  EX_zn2_e : 0.000108
  EX_ni2_e : 0.000102

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994924
  EX_h2o_e : 548.239935
  EX_co2_e : 22.875055
  EX_ac_e : 1.673875
  EX_glyclt_e : 0.945733
  Auxiliary production reaction : 0.945592
  DM_oxam_c : 0.000354
  DM_5drib_c : 0.000212
  DM_4crsol_c : 0.000070

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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