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 : fum_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (8 of 8: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b3553 b4269 b3942 b1732 b0493 b3588 b3003 b3011 b0474 b2518 b0871 b2925 b2097 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b2690 b2463 b2210 b1033 b3551 b1602 b4138 b4123 b0621 b4219 b1832 b1778 b1727 b0114 b2492 b0904 b1380 b1710 b2480 b1771 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.398554 (mmol/gDw/h)
  Minimum Production Rate : 0.414053 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.262497
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.304348
  EX_pi_e : 0.384447
  EX_so4_e : 0.100364
  EX_k_e : 0.077795
  EX_fe2_e : 0.006401
  EX_mg2_e : 0.003457
  EX_cl_e : 0.002074
  EX_ca2_e : 0.002074
  EX_cu2_e : 0.000283
  EX_mn2_e : 0.000275
  EX_zn2_e : 0.000136
  EX_ni2_e : 0.000129

Product: (mmol/gDw/h)
  EX_h2o_e : 47.051777
  EX_co2_e : 36.988827
  EX_h_e : 5.295655
  EX_etoh_e : 1.289861
  EX_3hpp_e : 0.805478
  EX_fum_e : 0.414053
  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.

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Last updated: 21-Sep-2023
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