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 : pyr_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (100 of 114: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b1478 b0474 b2518 b1241 b0351 b4069 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b2690 b3616 b3589 b0675 b0822 b2913 b0114 b0755 b3612 b2492 b0904 b0789 b1249 b0515   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.577586 (mmol/gDw/h)
  Minimum Production Rate : 0.593621 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.338890
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.762834
  EX_pi_e : 0.557142
  EX_so4_e : 0.145448
  EX_k_e : 0.112741
  EX_fe2_e : 0.009277
  EX_mg2_e : 0.005011
  EX_ca2_e : 0.003006
  EX_cl_e : 0.003006
  EX_cu2_e : 0.000410
  EX_mn2_e : 0.000399
  EX_zn2_e : 0.000197
  EX_ni2_e : 0.000187
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 48.645677
  EX_co2_e : 26.630939
  EX_h_e : 11.603669
  EX_ac_e : 2.178002
  EX_alltn_e : 0.881240
  EX_pyr_e : 0.593621
  DM_5drib_c : 0.000130
  DM_4crsol_c : 0.000129

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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