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 (76 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b3553 b1478 b3399 b1241 b4069 b4384 b2744 b3752 b3115 b1849 b2296 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b1779 b0207 b3012 b1982 b4139 b1033 b1623 b0261 b0411 b2799 b1602 b4381 b3915 b0452 b0509 b3125 b0529 b2492 b0904 b2954 b1781 b3001 b3029 b1380 b0325 b1301 b2660 b1771 b3662 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.424952 (mmol/gDw/h)
  Minimum Production Rate : 0.476786 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.408409
  EX_o2_e : 287.814571
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.975755
  EX_pi_e : 2.317056
  EX_so4_e : 0.107011
  EX_k_e : 0.082948
  EX_mg2_e : 0.003686
  EX_ca2_e : 0.002212
  EX_cl_e : 0.002212
  EX_cu2_e : 0.000301
  EX_mn2_e : 0.000294
  EX_zn2_e : 0.000145
  EX_ni2_e : 0.000137
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993175
  EX_h2o_e : 555.666625
  EX_co2_e : 37.291681
  Auxiliary production reaction : 0.476786
  EX_ac_e : 0.247401
  EX_ade_e : 0.000476
  DM_5drib_c : 0.000285
  DM_4crsol_c : 0.000095

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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