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 (97 of 114: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b1241 b0351 b4069 b3708 b0512 b0871 b2297 b2458 b2779 b2925 b2097 b3617 b2797 b3117 b1814 b4471 b3946 b0825 b4381 b0114 b2366 b0529 b2492 b0904 b1533 b1813   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.591242 (mmol/gDw/h)
  Minimum Production Rate : 0.139328 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.992289
  EX_nh4_e : 10.920414
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.570316
  EX_so4_e : 0.148887
  EX_k_e : 0.115406
  EX_fe2_e : 0.009496
  EX_mg2_e : 0.005129
  EX_ca2_e : 0.003077
  EX_cl_e : 0.003077
  EX_cu2_e : 0.000419
  EX_mn2_e : 0.000409
  EX_zn2_e : 0.000202
  EX_ni2_e : 0.000191
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 50.471701
  EX_co2_e : 26.782964
  EX_h_e : 12.104958
  EX_ac_e : 1.997815
  EX_alltn_e : 1.133762
  EX_pyr_e : 0.139328
  EX_glyc__R_e : 0.000198
  DM_5drib_c : 0.000133
  DM_4crsol_c : 0.000132

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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