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 : 12ppd__S_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (22 of 92: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b4467 b1241 b0351 b0871 b2779 b2925 b2097 b3844 b1004 b3713 b1109 b0046 b3236 b2690 b1302 b2662 b4015 b3945 b1602 b2913 b1727 b0529 b2492 b0904 b1380 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.381318 (mmol/gDw/h)
  Minimum Production Rate : 0.045089 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.240480
  EX_o2_e : 279.929122
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.118206
  EX_pi_e : 0.367822
  EX_so4_e : 0.096024
  EX_k_e : 0.074431
  EX_mg2_e : 0.003308
  EX_cl_e : 0.001985
  EX_ca2_e : 0.001985
  EX_cu2_e : 0.000270
  EX_mn2_e : 0.000263
  EX_zn2_e : 0.000130
  EX_ni2_e : 0.000123

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993876
  EX_h2o_e : 542.935741
  EX_co2_e : 29.597857
  EX_pyr_e : 4.249690
  EX_etoh_e : 0.933219
  EX_12ppd__S_e : 0.045089
  DM_5drib_c : 0.000086
  DM_4crsol_c : 0.000085

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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