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 : ppgpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (48 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b2836 b4384 b2744 b3708 b3008 b0871 b0030 b2407 b1779 b1982 b2797 b3117 b1814 b4471 b4374 b2361 b2291 b0261 b2406 b0114 b0886 b2366 b0529 b2492 b0904 b2578 b1533 b3927 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.688553 (mmol/gDw/h)
  Minimum Production Rate : 0.157992 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.161058
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.226269
  EX_pi_e : 1.296149
  EX_so4_e : 0.173391
  EX_k_e : 0.134401
  EX_fe2_e : 0.011059
  EX_mg2_e : 0.005973
  EX_ca2_e : 0.003584
  EX_cl_e : 0.003584
  EX_cu2_e : 0.000488
  EX_mn2_e : 0.000476
  EX_zn2_e : 0.000235
  EX_ni2_e : 0.000222
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 50.709271
  EX_co2_e : 30.156622
  EX_h_e : 6.800672
  Auxiliary production reaction : 0.157992
  DM_5drib_c : 0.000462
  DM_4crsol_c : 0.000154

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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