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 : 5caiz_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (41 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b1241 b0351 b4069 b4384 b2744 b2297 b2458 b3617 b0030 b2407 b3124 b1982 b3665 b4374 b2361 b2291 b0261 b0411 b0112 b2789 b3127 b0114 b0529 b2492 b0904 b0514 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.475923 (mmol/gDw/h)
  Minimum Production Rate : 1.824189 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.637120
  EX_nh4_e : 10.615160
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.283267
  EX_so4_e : 0.119847
  EX_k_e : 0.092897
  EX_fe2_e : 0.007644
  EX_mg2_e : 0.004129
  EX_ca2_e : 0.002477
  EX_cl_e : 0.002477
  EX_cu2_e : 0.000337
  EX_mn2_e : 0.000329
  EX_zn2_e : 0.000162
  EX_ni2_e : 0.000154
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 46.169641
  EX_co2_e : 19.002988
  EX_h_e : 14.192953
  EX_ac_e : 2.520245
  Auxiliary production reaction : 1.824189
  EX_ade_e : 0.000533
  DM_5drib_c : 0.000319
  EX_glyclt_e : 0.000318
  DM_4crsol_c : 0.000106

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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