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 (67 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b4467 b1478 b3942 b1732 b1241 b4069 b3115 b1849 b2296 b2779 b3844 b1851 b1004 b3713 b1109 b0046 b2463 b2210 b3551 b1602 b4219 b1832 b1778 b1380 b1710 b2480 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.572564 (mmol/gDw/h)
  Minimum Production Rate : 0.828853 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.294920
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.183643
  EX_pi_e : 0.552299
  EX_so4_e : 0.144183
  EX_k_e : 0.111760
  EX_fe2_e : 0.009196
  EX_mg2_e : 0.004967
  EX_ca2_e : 0.002980
  EX_cl_e : 0.002980
  EX_cu2_e : 0.000406
  EX_mn2_e : 0.000396
  EX_zn2_e : 0.000195
  EX_ni2_e : 0.000185
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 47.636618
  EX_co2_e : 33.345637
  EX_h_e : 5.594286
  EX_12ppd__R_e : 0.828853
  EX_ac_e : 0.333339
  DM_5drib_c : 0.000129
  DM_4crsol_c : 0.000128

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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