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 : glyclt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (47 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4467 b4382 b1241 b0351 b4069 b4384 b2297 b2458 b2779 b2926 b3617 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b0261 b1602 b2913 b1727 b2975 b0114 b3603 b0529 b2492 b0904 b1380 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.399691 (mmol/gDw/h)
  Minimum Production Rate : 0.221759 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.773658
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.316624
  EX_pi_e : 0.385544
  EX_so4_e : 0.100650
  EX_k_e : 0.078017
  EX_fe2_e : 0.006419
  EX_mg2_e : 0.003467
  EX_ca2_e : 0.002080
  EX_cl_e : 0.002080
  EX_cu2_e : 0.000283
  EX_mn2_e : 0.000276
  EX_zn2_e : 0.000136
  EX_ni2_e : 0.000129

Product: (mmol/gDw/h)
  EX_h2o_e : 48.934210
  EX_co2_e : 38.379488
  EX_h_e : 6.143804
  EX_ac_e : 1.977053
  EX_glyc__R_e : 0.272476
  Auxiliary production reaction : 0.221759
  DM_5drib_c : 0.000090
  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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