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 : dnad_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (17 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b1241 b0351 b4069 b4384 b2297 b2458 b2779 b1850 b3617 b0030 b2407 b1982 b3665 b0261 b0507 b2913 b4381 b2406 b0112 b0114 b0529 b2492 b0904 b1380 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.398132 (mmol/gDw/h)
  Minimum Production Rate : 0.763009 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.133548
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.880074
  EX_pi_e : 1.910059
  EX_so4_e : 0.100258
  EX_k_e : 0.077713
  EX_fe2_e : 0.006394
  EX_mg2_e : 0.003454
  EX_ca2_e : 0.002072
  EX_cl_e : 0.002072
  EX_cu2_e : 0.000282
  EX_mn2_e : 0.000275
  EX_zn2_e : 0.000136
  EX_ni2_e : 0.000129

Product: (mmol/gDw/h)
  EX_h2o_e : 49.471188
  EX_co2_e : 23.692984
  EX_h_e : 8.682069
  EX_ac_e : 1.969343
  Auxiliary production reaction : 0.763009
  EX_ade_e : 0.000446
  DM_5drib_c : 0.000267
  EX_glyclt_e : 0.000266
  DM_4crsol_c : 0.000089

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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