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 : cdigmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4382 b3942 b1732 b4069 b4384 b3708 b2930 b4232 b3697 b3925 b2297 b2458 b2779 b0030 b2407 b3236 b2690 b1982 b2797 b3117 b1814 b4471 b2210 b2440 b3945 b2406 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b0515 b3662 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.609330 (mmol/gDw/h)
  Minimum Production Rate : 0.128252 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.682170
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.872756
  EX_pi_e : 0.844269
  EX_so4_e : 0.153442
  EX_k_e : 0.118937
  EX_fe2_e : 0.009786
  EX_mg2_e : 0.005286
  EX_ca2_e : 0.003172
  EX_cl_e : 0.003172
  EX_cu2_e : 0.000432
  EX_mn2_e : 0.000421
  EX_zn2_e : 0.000208
  EX_ni2_e : 0.000197
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 45.750214
  EX_co2_e : 26.308270
  EX_h_e : 8.784468
  EX_glyc__R_e : 1.795419
  EX_ac_e : 0.354744
  Auxiliary production reaction : 0.128252
  EX_alltn_e : 0.002379
  DM_mththf_c : 0.001970
  DM_5drib_c : 0.000409
  DM_4crsol_c : 0.000136

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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