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 : glyc__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (15 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3708 b3752 b2297 b2458 b3617 b2407 b3124 b1982 b2797 b3117 b1814 b4471 b0261 b2406 b0112 b2789 b3127 b0452 b0114 b2366 b2492 b0904 b1533 b0514 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.524373 (mmol/gDw/h)
  Minimum Production Rate : 0.356666 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.708935
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.377099
  EX_pi_e : 0.505813
  EX_so4_e : 0.132048
  EX_k_e : 0.102354
  EX_fe2_e : 0.008422
  EX_mg2_e : 0.004549
  EX_cl_e : 0.002729
  EX_ca2_e : 0.002729
  EX_cu2_e : 0.000372
  EX_mn2_e : 0.000362
  EX_zn2_e : 0.000179
  EX_ni2_e : 0.000169
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 40.420418
  EX_co2_e : 23.005352
  EX_h_e : 8.808934
  EX_ac_e : 2.205935
  DM_oxam_c : 0.713919
  DM_5drib_c : 0.713684
  DM_4crsol_c : 0.713449
  Auxiliary production reaction : 0.356666
  EX_glyclt_e : 0.000351

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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