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 : cph4_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (27 of 43: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b4069 b4384 b2744 b3708 b2297 b2458 b0030 b2883 b1982 b2797 b3117 b1814 b4471 b0261 b4381 b2868 b4064 b4464 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b2835 b0494   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.754314 (mmol/gDw/h)
  Minimum Production Rate : 0.319862 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.696089
  EX_o2_e : 275.267115
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.748372
  EX_pi_e : 0.727616
  EX_so4_e : 0.189951
  EX_k_e : 0.147237
  EX_mg2_e : 0.006544
  EX_ca2_e : 0.003926
  EX_cl_e : 0.003926
  EX_cu2_e : 0.000535
  EX_mn2_e : 0.000521
  EX_zn2_e : 0.000257
  EX_ni2_e : 0.000244
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_fe3_e : 999.987885
  EX_h2o_e : 549.035989
  EX_co2_e : 25.919010
  EX_ac_e : 0.439151
  Auxiliary production reaction : 0.319862
  EX_ade_e : 0.000508
  DM_5drib_c : 0.000170
  DM_4crsol_c : 0.000168

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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