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 (38 of 120: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b3553 b4382 b3846 b2341 b1241 b0351 b4069 b4384 b3708 b3752 b3115 b1849 b2296 b3617 b2407 b1982 b2797 b3117 b1814 b4471 b1033 b4014 b0261 b2976 b0507 b3709 b2406 b3161 b0112 b0452 b0114 b1539 b2492 b0904 b3035 b1533 b1473 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.354413 (mmol/gDw/h)
  Minimum Production Rate : 1.060539 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 20.261127
  EX_nh4_e : 11.251802
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.341869
  EX_so4_e : 0.089248
  EX_k_e : 0.069179
  EX_fe2_e : 0.005692
  EX_mg2_e : 0.003075
  EX_ca2_e : 0.001845
  EX_cl_e : 0.001845
  EX_cu2_e : 0.000251
  EX_mn2_e : 0.000245
  EX_zn2_e : 0.000121
  EX_ni2_e : 0.000114

Product: (mmol/gDw/h)
  EX_h2o_e : 46.815038
  EX_co2_e : 18.365470
  EX_h_e : 14.679161
  EX_ac_e : 1.876790
  EX_glyclt_e : 1.060776
  Auxiliary production reaction : 1.060539
  DM_oxam_c : 0.000397
  DM_5drib_c : 0.000238
  DM_4crsol_c : 0.000079

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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