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 : 12ppd__R_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3553 b3942 b1732 b1241 b0351 b0871 b2925 b2097 b1004 b3713 b1109 b0046 b2463 b3946 b2210 b0825 b1033 b1493 b3517 b1602 b1727 b2492 b0904 b1380 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.464290 (mmol/gDw/h)
  Minimum Production Rate : 3.417246 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 26.282332
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.014293
  EX_pi_e : 0.447857
  EX_so4_e : 0.116918
  EX_k_e : 0.090626
  EX_mg2_e : 0.004028
  EX_fe2_e : 0.003832
  EX_fe3_e : 0.003625
  EX_ca2_e : 0.002417
  EX_cl_e : 0.002417
  EX_cu2_e : 0.000329
  EX_mn2_e : 0.000321
  EX_zn2_e : 0.000158
  EX_ni2_e : 0.000150
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 39.532846
  EX_co2_e : 30.691288
  EX_h_e : 4.269707
  EX_12ppd__R_e : 3.417246
  DM_5drib_c : 0.000104
  DM_4crsol_c : 0.000104

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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