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 (101 of 114: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3553 b1241 b0351 b2930 b4232 b3697 b3925 b0871 b3115 b1849 b2296 b2926 b2690 b1525 b1033 b2661 b4014 b2976 b0614 b0726 b3945 b0507 b2913 b0452 b1539 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.399559 (mmol/gDw/h)
  Minimum Production Rate : 4.102035 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.696757
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.315202
  EX_pi_e : 0.385417
  EX_so4_e : 0.100617
  EX_k_e : 0.077991
  EX_fe2_e : 0.006417
  EX_mg2_e : 0.003466
  EX_ca2_e : 0.002080
  EX_cl_e : 0.002080
  EX_cu2_e : 0.000283
  EX_mn2_e : 0.000276
  EX_zn2_e : 0.000136
  EX_ni2_e : 0.000129

Product: (mmol/gDw/h)
  EX_h2o_e : 44.151554
  EX_co2_e : 29.498273
  EX_h_e : 8.670676
  EX_pyr_e : 4.102035
  EX_ac_e : 0.897067
  EX_glyclt_e : 0.000267
  EX_mththf_e : 0.000179
  DM_5drib_c : 0.000090
  DM_4crsol_c : 0.000089

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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