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_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (67 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b4467 b3399 b4269 b0493 b3588 b3003 b3011 b2744 b0871 b0160 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b4374 b0675 b2361 b2291 b0261 b2799 b3945 b1602 b3915 b1727 b0114 b0529 b2492 b0904 b3927 b1380 b2660 b0606 b2285 b1009 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.484431 (mmol/gDw/h)
  Minimum Production Rate : 0.103498 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.215596
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.647862
  EX_pi_e : 0.467285
  EX_so4_e : 0.121990
  EX_k_e : 0.094558
  EX_fe3_e : 0.007782
  EX_mg2_e : 0.004202
  EX_ca2_e : 0.002521
  EX_cl_e : 0.002521
  EX_cu2_e : 0.000343
  EX_mn2_e : 0.000335
  EX_zn2_e : 0.000165
  EX_ni2_e : 0.000156
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.181724
  EX_co2_e : 38.146613
  EX_h_e : 4.978445
  EX_hxan_e : 0.104011
  DM_5drib_c : 0.103794
  DM_4crsol_c : 0.103577
  EX_glyclt_e : 0.103469

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.

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Last updated: 21-Sep-2023
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