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 : duri_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (25 of 50: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3942 b1732 b1241 b0351 b4069 b4384 b0871 b2297 b2458 b2779 b2925 b2097 b3617 b0030 b2407 b3236 b2690 b1982 b2210 b3945 b2913 b4381 b2406 b0114 b0529 b2492 b0904 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.284484 (mmol/gDw/h)
  Minimum Production Rate : 1.090793 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.775262
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.254177
  EX_pi_e : 0.274415
  EX_so4_e : 0.071639
  EX_k_e : 0.055529
  EX_fe2_e : 0.004569
  EX_mg2_e : 0.002468
  EX_ca2_e : 0.001481
  EX_cl_e : 0.001481
  EX_cu2_e : 0.000202
  EX_mn2_e : 0.000197
  EX_zn2_e : 0.000097
  EX_ni2_e : 0.000092

Product: (mmol/gDw/h)
  EX_h2o_e : 44.046772
  EX_co2_e : 26.593256
  EX_h_e : 9.053816
  EX_pyr_e : 3.395947
  Auxiliary production reaction : 1.090793
  EX_ac_e : 0.861855
  DM_oxam_c : 0.000191
  DM_mththf_c : 0.000127
  EX_glyc__R_e : 0.000095
  DM_5drib_c : 0.000064
  DM_4crsol_c : 0.000063

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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