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 : gdpmann_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 108: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3708 b0910 b3752 b2297 b2458 b2407 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b2440 b0261 b2406 b0112 b0114 b2366 b2492 b0904 b1533 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.423585 (mmol/gDw/h)
  Minimum Production Rate : 0.633763 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.251014
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.743968
  EX_pi_e : 1.676119
  EX_so4_e : 0.106667
  EX_k_e : 0.082681
  EX_fe2_e : 0.006803
  EX_mg2_e : 0.003675
  EX_ca2_e : 0.002205
  EX_cl_e : 0.002205
  EX_cu2_e : 0.000300
  EX_mn2_e : 0.000293
  EX_zn2_e : 0.000144
  EX_ni2_e : 0.000137
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 49.312378
  EX_co2_e : 29.253046
  EX_h_e : 7.403625
  EX_ac_e : 1.609323
  Auxiliary production reaction : 0.633763
  DM_oxam_c : 0.000474
  DM_5drib_c : 0.000284
  DM_4crsol_c : 0.000094

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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