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 : bwco1gdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (37 of 96: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3399 b2744 b3708 b3008 b0871 b2883 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0411 b4381 b2406 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b3821 b0516 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.788549 (mmol/gDw/h)
  Minimum Production Rate : 0.028383 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.572026
  EX_o2_e : 275.101697
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.026663
  EX_pi_e : 0.845788
  EX_so4_e : 0.312104
  EX_k_e : 0.153919
  EX_tungs_e : 0.028383
  EX_mg2_e : 0.006841
  EX_ca2_e : 0.004104
  EX_cl_e : 0.004104
  EX_cu2_e : 0.000559
  EX_mn2_e : 0.000545
  EX_zn2_e : 0.000269
  EX_ni2_e : 0.000255
  EX_cobalt2_e : 0.000020

Product: (mmol/gDw/h)
  EX_fe3_e : 999.987335
  EX_h2o_e : 548.909834
  EX_co2_e : 26.695769
  Auxiliary production reaction : 0.028383
  EX_alltn_e : 0.021164
  EX_mththf_e : 0.000353
  DM_5drib_c : 0.000177
  DM_4crsol_c : 0.000176

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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