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 : dcdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (81 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 50
  Gene deletion: b3553 b3399 b4382 b3942 b1732 b1241 b0351 b4069 b2502 b4384 b2744 b3708 b2930 b4232 b3697 b3925 b0512 b0871 b2297 b2458 b2926 b3617 b1004 b3713 b1109 b0046 b3236 b1982 b2797 b3117 b1814 b4471 b3946 b2210 b0825 b1033 b0675 b2361 b2291 b1602 b2406 b0114 b2366 b2492 b0904 b1533 b1380 b1511 b0221 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.296330 (mmol/gDw/h)
  Minimum Production Rate : 0.188036 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 29.462945
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.862531
  EX_pi_e : 0.661913
  EX_so4_e : 0.074622
  EX_k_e : 0.057842
  EX_fe2_e : 0.004759
  EX_mg2_e : 0.002571
  EX_ca2_e : 0.001542
  EX_cl_e : 0.001542
  EX_cu2_e : 0.000210
  EX_mn2_e : 0.000205
  EX_zn2_e : 0.000101
  EX_ni2_e : 0.000096

Product: (mmol/gDw/h)
  EX_h2o_e : 45.196414
  EX_co2_e : 26.932319
  EX_h_e : 10.429847
  EX_pyr_e : 4.550545
  EX_his__L_e : 0.699094
  EX_ac_e : 0.682348
  Auxiliary production reaction : 0.188036
  EX_alltn_e : 0.000199
  DM_mththf_c : 0.000133
  DM_5drib_c : 0.000067
  DM_4crsol_c : 0.000066

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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