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 : dcmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (53 of 117: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3752 b0871 b2779 b2925 b2097 b3617 b2407 b3236 b0907 b1982 b3946 b0825 b2406 b0112 b2789 b3127 b2868 b0114 b0529 b2492 b0904 b1380 b3662 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.445963 (mmol/gDw/h)
  Minimum Production Rate : 1.450317 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 25.344559
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.168815
  EX_pi_e : 1.880496
  EX_so4_e : 0.112302
  EX_k_e : 0.087049
  EX_fe2_e : 0.007163
  EX_mg2_e : 0.003869
  EX_ca2_e : 0.002321
  EX_cl_e : 0.002321
  EX_cu2_e : 0.000316
  EX_mn2_e : 0.000308
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 48.986161
  EX_co2_e : 25.177730
  EX_h_e : 8.876579
  Auxiliary production reaction : 1.450317
  EX_acald_e : 1.091529
  EX_pyr_e : 0.426242
  EX_ade_e : 0.000300
  DM_mththf_c : 0.000200
  EX_glyclt_e : 0.000199
  DM_5drib_c : 0.000100
  DM_4crsol_c : 0.000099

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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