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 (119 of 120: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 68
  Gene deletion: b3553 b1478 b4269 b0493 b3588 b3003 b3011 b0474 b2518 b1241 b0351 b4069 b4384 b3708 b1479 b0871 b3115 b1849 b2296 b2779 b2925 b2097 b0030 b2407 b1238 b3236 b0907 b2690 b3962 b1982 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b1033 b0595 b1415 b1014 b4014 b0261 b2976 b3945 b0507 b3709 b1907 b4381 b2406 b3161 b0112 b2868 b4265 b0114 b2366 b2492 b0904 b1533 b3821 b1380 b0325 b2413 b1473 b4266 b3662 b1813   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.198595 (mmol/gDw/h)
  Minimum Production Rate : 0.422344 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.295801
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.274034
  EX_so4_e : 0.221938
  EX_pi_e : 0.191566
  EX_k_e : 0.038764
  EX_fe2_e : 0.003190
  EX_mg2_e : 0.001723
  EX_ca2_e : 0.001034
  EX_cl_e : 0.001034
  EX_cu2_e : 0.000141
  EX_mn2_e : 0.000137
  EX_zn2_e : 0.000068
  EX_ni2_e : 0.000064

Product: (mmol/gDw/h)
  EX_h2o_e : 43.637452
  EX_co2_e : 26.677044
  EX_h_e : 9.510479
  EX_pyr_e : 3.768017
  EX_acald_e : 0.936082
  EX_dxylnt_e : 0.422432
  Auxiliary production reaction : 0.422344
  EX_ac_e : 0.287547
  EX_met__L_e : 0.171928
  EX_hxan_e : 0.000222
  DM_5drib_c : 0.000133
  DM_4crsol_c : 0.000044

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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