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 : gua_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b0469 b3942 b1732 b0474 b1241 b0351 b4069 b2744 b1479 b2297 b2458 b2779 b2926 b3617 b3236 b2883 b2463 b3962 b0104 b2210 b4267 b1415 b3551 b1014 b3945 b4219 b1832 b1778 b4381 b2868 b0114 b0529 b2492 b0904 b1380 b0325 b1710 b2480 b0508 b4266 b1813 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.421131 (mmol/gDw/h)
  Minimum Production Rate : 0.108955 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 38.825944
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.092949
  EX_pi_e : 0.406225
  EX_so4_e : 0.106049
  EX_k_e : 0.082202
  EX_fe3_e : 0.006764
  EX_mg2_e : 0.003653
  EX_ca2_e : 0.002192
  EX_cl_e : 0.002192
  EX_cu2_e : 0.000299
  EX_mn2_e : 0.000291
  EX_zn2_e : 0.000144
  EX_ni2_e : 0.000136
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 51.606394
  EX_co2_e : 39.399331
  EX_h_e : 5.805840
  EX_ac_e : 1.384504
  EX_gua_e : 0.108955
  EX_dxylnt_e : 0.000282
  DM_5drib_c : 0.000095
  DM_4crsol_c : 0.000094

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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