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 (51 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b4467 b4269 b0493 b3588 b3003 b3011 b0474 b2518 b0871 b2779 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b4139 b3945 b1602 b0507 b1727 b2975 b3603 b0529 b2492 b0904 b3029 b1380 b2660 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.494450 (mmol/gDw/h)
  Minimum Production Rate : 0.176624 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 38.384039
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.340016
  EX_pi_e : 0.476949
  EX_so4_e : 0.124512
  EX_k_e : 0.096513
  EX_mg2_e : 0.004289
  EX_fe2_e : 0.004081
  EX_fe3_e : 0.003861
  EX_ca2_e : 0.002574
  EX_cl_e : 0.002574
  EX_cu2_e : 0.000351
  EX_mn2_e : 0.000342
  EX_zn2_e : 0.000169
  EX_ni2_e : 0.000160
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.406981
  EX_co2_e : 39.351858
  EX_h_e : 4.723687
  Auxiliary production reaction : 0.176624
  DM_5drib_c : 0.000111
  DM_4crsol_c : 0.000110

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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