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 : amet_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (38 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b4384 b2744 b3708 b3008 b0871 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b0261 b4381 b2239 b3453 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b2835 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.784291 (mmol/gDw/h)
  Minimum Production Rate : 0.090011 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.782672
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.010344
  EX_pi_e : 0.756532
  EX_so4_e : 0.287511
  EX_k_e : 0.153088
  EX_fe2_e : 0.012596
  EX_mg2_e : 0.006804
  EX_ca2_e : 0.004082
  EX_cl_e : 0.004082
  EX_cu2_e : 0.000556
  EX_mn2_e : 0.000542
  EX_zn2_e : 0.000267
  EX_ni2_e : 0.000253
  EX_cobalt2_e : 0.000020

Product: (mmol/gDw/h)
  EX_h2o_e : 48.427654
  EX_co2_e : 26.456540
  EX_h_e : 7.476412
  Auxiliary production reaction : 0.090011
  DM_5drib_c : 0.000526
  DM_4crsol_c : 0.000175

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.

Last updated: 21-Sep-2023
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