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 : idp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b2836 b3399 b4384 b2744 b3708 b3008 b2930 b4232 b3697 b3925 b0871 b2779 b2407 b2690 b1982 b2797 b3117 b1814 b4471 b3665 b4374 b0675 b2361 b2291 b3945 b0114 b1539 b2492 b0904 b1533 b3927 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.644175 (mmol/gDw/h)
  Minimum Production Rate : 0.148192 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 26.504966
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.551971
  EX_pi_e : 0.917760
  EX_so4_e : 0.162216
  EX_k_e : 0.125738
  EX_fe2_e : 0.010346
  EX_mg2_e : 0.005588
  EX_cl_e : 0.003353
  EX_ca2_e : 0.003353
  EX_cu2_e : 0.000457
  EX_mn2_e : 0.000445
  EX_zn2_e : 0.000220
  EX_ni2_e : 0.000208
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 45.388413
  EX_co2_e : 26.594891
  EX_h_e : 8.192066
  EX_glyc__R_e : 1.826385
  Auxiliary production reaction : 0.148192
  EX_ade_e : 0.000434
  DM_mththf_c : 0.000289
  DM_5drib_c : 0.000145
  DM_4crsol_c : 0.000144

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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