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__S_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (86 of 92: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b3553 b1478 b1241 b0351 b0871 b2779 b2925 b2097 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b0207 b3012 b1302 b2662 b4139 b3946 b0825 b1033 b4014 b2976 b1602 b2223 b4381 b2789 b3127 b2492 b0904 b1781 b3001 b3029 b1380 b0325 b2660 b1771 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.462968 (mmol/gDw/h)
  Minimum Production Rate : 1.194022 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.225805
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.000010
  EX_pi_e : 0.446581
  EX_so4_e : 0.116584
  EX_k_e : 0.090368
  EX_fe2_e : 0.007436
  EX_mg2_e : 0.004016
  EX_ca2_e : 0.002410
  EX_cl_e : 0.002410
  EX_cu2_e : 0.000328
  EX_mn2_e : 0.000320
  EX_zn2_e : 0.000158
  EX_ni2_e : 0.000150
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 48.439479
  EX_co2_e : 37.409668
  EX_h_e : 4.253930
  EX_12ppd__S_e : 1.195881
  DM_5drib_c : 0.000104
  DM_4crsol_c : 0.000103

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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