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 (83 of 92: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b4467 b0474 b1241 b0351 b0871 b2779 b2925 b2097 b1004 b3713 b1109 b0046 b3236 b1638 b2690 b3908 b1656 b0207 b3012 b0477 b4139 b1493 b3517 b4015 b1602 b2913 b2223 b3915 b1727 b2492 b0904 b1781 b3001 b1380 b0325 b1301 b1771 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.469478 (mmol/gDw/h)
  Minimum Production Rate : 1.052081 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.517986
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.070326
  EX_pi_e : 0.452862
  EX_so4_e : 0.118224
  EX_k_e : 0.091639
  EX_fe3_e : 0.007540
  EX_mg2_e : 0.004073
  EX_ca2_e : 0.002444
  EX_cl_e : 0.002444
  EX_cu2_e : 0.000333
  EX_mn2_e : 0.000324
  EX_zn2_e : 0.000160
  EX_ni2_e : 0.000152
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 48.915601
  EX_co2_e : 37.573828
  EX_h_e : 4.321294
  EX_12ppd__S_e : 1.052081
  DM_5drib_c : 0.000106
  DM_4crsol_c : 0.000105

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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