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 : fprica_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b3553 b4069 b4384 b3752 b2297 b2458 b2779 b2925 b2097 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b2690 b3908 b1656 b1982 b4139 b1033 b3665 b0411 b1602 b4381 b1727 b0114 b0529 b2492 b0904 b1380 b2660 b1771 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.399039 (mmol/gDw/h)
  Minimum Production Rate : 0.184391 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.355842
  EX_o2_e : 290.919006
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.048491
  EX_pi_e : 0.569306
  EX_so4_e : 0.100486
  EX_k_e : 0.077890
  EX_mg2_e : 0.003462
  EX_ca2_e : 0.002077
  EX_cl_e : 0.002077
  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_fe3_e : 999.993591
  EX_h2o_e : 553.691418
  EX_co2_e : 41.310517
  EX_ac_e : 0.232315
  Auxiliary production reaction : 0.184391
  EX_ade_e : 0.000269
  DM_mththf_c : 0.000179
  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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