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 : xtp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (50 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b0512 b0871 b2926 b0160 b0907 b1982 b3616 b3589 b0675 b2361 b0261 b4381 b0112 b0114 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.512563 (mmol/gDw/h)
  Minimum Production Rate : 0.819698 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.895008
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.870370
  EX_pi_e : 2.953516
  EX_so4_e : 0.129074
  EX_k_e : 0.100049
  EX_fe2_e : 0.008232
  EX_mg2_e : 0.004446
  EX_ca2_e : 0.002668
  EX_cl_e : 0.002668
  EX_cu2_e : 0.000363
  EX_mn2_e : 0.000354
  EX_zn2_e : 0.000175
  EX_ni2_e : 0.000166
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 50.821172
  EX_co2_e : 26.531830
  EX_h_e : 6.404970
  EX_acald_e : 2.087876
  Auxiliary production reaction : 0.819698
  EX_alltn_e : 0.013985
  DM_5drib_c : 0.000344
  DM_4crsol_c : 0.000114

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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