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 : 5apru_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (93 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3399 b4382 b2502 b4384 b2744 b3708 b3008 b0871 b2407 b0120 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b0114 b0886 b0529 b1539 b2492 b0904 b2578 b1533 b3927 b3825 b0494 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.763712 (mmol/gDw/h)
  Minimum Production Rate : 0.039859 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.643043
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.853641
  EX_pi_e : 0.776540
  EX_so4_e : 0.192318
  EX_k_e : 0.149071
  EX_fe2_e : 0.012266
  EX_mg2_e : 0.006625
  EX_cl_e : 0.003975
  EX_ca2_e : 0.003975
  EX_cu2_e : 0.000541
  EX_mn2_e : 0.000528
  EX_zn2_e : 0.000260
  EX_ni2_e : 0.000247
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 47.926591
  EX_co2_e : 26.061799
  EX_h_e : 7.622906
  EX_thymd_e : 0.223089
  Auxiliary production reaction : 0.039859
  DM_5drib_c : 0.000512
  DM_4crsol_c : 0.000170

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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