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 : dudp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (41 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3942 b1732 b1241 b0351 b4069 b4384 b2744 b1479 b2930 b4232 b3697 b3925 b0871 b3115 b1849 b2296 b2926 b3617 b0030 b2407 b3236 b2463 b1982 b3946 b2210 b0825 b4374 b2361 b2291 b0114 b0529 b2492 b0904 b1380 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.458342 (mmol/gDw/h)
  Minimum Production Rate : 1.476766 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.720419
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.465184
  EX_pi_e : 3.395651
  EX_so4_e : 0.115420
  EX_k_e : 0.089465
  EX_fe2_e : 0.007361
  EX_mg2_e : 0.003976
  EX_ca2_e : 0.002386
  EX_cl_e : 0.002386
  EX_cu2_e : 0.000325
  EX_mn2_e : 0.000317
  EX_zn2_e : 0.000156
  EX_ni2_e : 0.000148
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 50.192004
  EX_co2_e : 24.870492
  EX_h_e : 7.060563
  Auxiliary production reaction : 1.476766
  EX_ac_e : 0.810461
  EX_ins_e : 0.140324
  DM_oxam_c : 0.000308
  DM_mththf_c : 0.000205
  DM_5drib_c : 0.000103
  DM_4crsol_c : 0.000102

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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