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 : pyr_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (105 of 114: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b1478 b1241 b0351 b2221 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b2690 b2388 b1302 b2662 b0675 b3565 b4015 b0822 b0614 b0726 b4388 b2587 b0755 b3612 b1539 b1492 b1912 b1813   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.664109 (mmol/gDw/h)
  Minimum Production Rate : 0.196967 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.848227
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.172317
  EX_pi_e : 0.640603
  EX_so4_e : 0.167236
  EX_k_e : 0.129629
  EX_fe2_e : 0.010666
  EX_mg2_e : 0.005761
  EX_ca2_e : 0.003457
  EX_cl_e : 0.003457
  EX_cu2_e : 0.000471
  EX_mn2_e : 0.000459
  EX_zn2_e : 0.000226
  EX_ni2_e : 0.000215
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 46.901205
  EX_co2_e : 29.166965
  EX_h_e : 7.790081
  EX_ac_e : 1.491019
  EX_pyr_e : 0.196967
  EX_mththf_e : 0.000298
  DM_5drib_c : 0.000149
  DM_4crsol_c : 0.000148

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.

Last updated: 21-Sep-2023
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