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 : seramp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (69 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3399 b1241 b0351 b2744 b3708 b3008 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b3617 b0160 b0517 b1779 b2690 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b3945 b0114 b2366 b2492 b0904 b1533 b3821 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.626448 (mmol/gDw/h)
  Minimum Production Rate : 0.086583 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 26.811121
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.285078
  EX_pi_e : 0.690858
  EX_so4_e : 0.157752
  EX_k_e : 0.122278
  EX_fe2_e : 0.010061
  EX_mg2_e : 0.005434
  EX_ca2_e : 0.003261
  EX_cl_e : 0.003261
  EX_cu2_e : 0.000444
  EX_mn2_e : 0.000433
  EX_zn2_e : 0.000214
  EX_ni2_e : 0.000202
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 46.697534
  EX_co2_e : 26.833826
  EX_h_e : 8.211181
  EX_pyr_e : 2.108799
  Auxiliary production reaction : 0.086583
  DM_mththf_c : 0.000281
  DM_5drib_c : 0.000141
  DM_4crsol_c : 0.000140

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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