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 : dudp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (27 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3399 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b0871 b2883 b3616 b3589 b3665 b0675 b2361 b0411 b4381 b0112 b3654 b3714 b3664 b0114 b0529 b2492 b0904 b1511 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.562585 (mmol/gDw/h)
  Minimum Production Rate : 1.335697 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 20.321972
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.736546
  EX_pi_e : 3.214066
  EX_so4_e : 0.141670
  EX_k_e : 0.109813
  EX_fe2_e : 0.009036
  EX_mg2_e : 0.004880
  EX_ca2_e : 0.002928
  EX_cl_e : 0.002928
  EX_cu2_e : 0.000399
  EX_mn2_e : 0.000389
  EX_zn2_e : 0.000192
  EX_ni2_e : 0.000182
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 48.449260
  EX_co2_e : 19.939522
  EX_h_e : 7.494236
  Auxiliary production reaction : 1.335697
  EX_thymd_e : 0.494643
  DM_mththf_c : 0.000252
  DM_5drib_c : 0.000127
  DM_4crsol_c : 0.000125

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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