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 (34 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b3115 b1849 b2296 b0160 b3616 b3589 b1623 b3665 b0675 b2361 b4381 b2406 b0112 b3654 b3714 b3664 b0114 b0529 b2492 b0904 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.574141 (mmol/gDw/h)
  Minimum Production Rate : 1.086074 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.724791
  EX_nh4_e : 11.631048
  EX_glc__D_e : 10.000000
  EX_pi_e : 4.898118
  EX_so4_e : 0.144580
  EX_k_e : 0.112068
  EX_fe2_e : 0.009221
  EX_mg2_e : 0.004981
  EX_ca2_e : 0.002988
  EX_cl_e : 0.002988
  EX_cu2_e : 0.000407
  EX_mn2_e : 0.000397
  EX_zn2_e : 0.000196
  EX_ni2_e : 0.000185
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 53.144393
  EX_co2_e : 21.691797
  EX_h_e : 10.473819
  EX_ac_e : 1.940158
  Auxiliary production reaction : 1.086074
  DM_mththf_c : 0.000257
  DM_5drib_c : 0.000129
  DM_4crsol_c : 0.000128

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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