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 (65 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b3708 b3008 b0871 b3617 b2407 b1238 b2797 b3117 b1814 b4471 b1623 b3665 b4381 b2406 b0112 b3654 b3714 b3664 b0114 b2366 b2492 b0904 b1533 b4141 b1798 b3662 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.619475 (mmol/gDw/h)
  Minimum Production Rate : 0.747359 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.486709
  EX_nh4_e : 10.427069
  EX_glc__D_e : 10.000000
  EX_pi_e : 3.586985
  EX_so4_e : 0.155996
  EX_k_e : 0.120917
  EX_fe2_e : 0.009949
  EX_mg2_e : 0.005374
  EX_ca2_e : 0.003224
  EX_cl_e : 0.003224
  EX_cu2_e : 0.000439
  EX_mn2_e : 0.000428
  EX_zn2_e : 0.000211
  EX_ni2_e : 0.000200
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 51.041968
  EX_co2_e : 23.472969
  EX_h_e : 7.934058
  EX_acald_e : 1.812732
  Auxiliary production reaction : 0.747359
  DM_mththf_c : 0.000278
  DM_5drib_c : 0.000139
  DM_4crsol_c : 0.000138

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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