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 (34 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b3399 b3942 b1732 b1241 b0351 b4069 b2744 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b2926 b3617 b0160 b3236 b2690 b1982 b2210 b0675 b2361 b3945 b4381 b2406 b0112 b2868 b0114 b0529 b2492 b0904 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.286801 (mmol/gDw/h)
  Minimum Production Rate : 1.084670 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 29.095097
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.382421
  EX_pi_e : 2.445990
  EX_so4_e : 0.072222
  EX_k_e : 0.055982
  EX_fe2_e : 0.004606
  EX_mg2_e : 0.002488
  EX_ca2_e : 0.001493
  EX_cl_e : 0.001493
  EX_cu2_e : 0.000203
  EX_mn2_e : 0.000198
  EX_zn2_e : 0.000098
  EX_ni2_e : 0.000093

Product: (mmol/gDw/h)
  EX_h2o_e : 47.799363
  EX_co2_e : 26.804706
  EX_h_e : 8.851932
  EX_pyr_e : 3.589531
  Auxiliary production reaction : 1.084670
  EX_ac_e : 0.426834
  EX_xan_e : 0.007504
  EX_ade_e : 0.000193
  DM_mththf_c : 0.000128
  DM_5drib_c : 0.000065
  DM_4crsol_c : 0.000064

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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