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 (44 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b2836 b3399 b2502 b2744 b3708 b3008 b0871 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b2291 b0261 b4381 b2943 b0114 b0886 b0529 b1539 b2492 b0904 b2578 b1533 b3927   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.757126 (mmol/gDw/h)
  Minimum Production Rate : 0.173726 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 26.089805
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.045524
  EX_pi_e : 1.425232
  EX_so4_e : 0.190659
  EX_k_e : 0.147786
  EX_fe2_e : 0.012160
  EX_mg2_e : 0.006568
  EX_ca2_e : 0.003941
  EX_cl_e : 0.003941
  EX_cu2_e : 0.000537
  EX_mn2_e : 0.000523
  EX_zn2_e : 0.000258
  EX_ni2_e : 0.000245
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 49.784006
  EX_co2_e : 27.184517
  EX_h_e : 7.477952
  Auxiliary production reaction : 0.173726
  DM_5drib_c : 0.000508
  DM_4crsol_c : 0.000169

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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