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 : didp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (50 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b1241 b0351 b3831 b4069 b4384 b3752 b3115 b1849 b2296 b2779 b2925 b2097 b3617 b2407 b3236 b2690 b2498 b0261 b3945 b2913 b2868 b0114 b0529 b2492 b0904 b1380   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.492651 (mmol/gDw/h)
  Minimum Production Rate : 0.629582 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.370029
  EX_o2_e : 277.278104
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.840574
  EX_pi_e : 1.734378
  EX_so4_e : 0.124059
  EX_k_e : 0.096162
  EX_mg2_e : 0.004274
  EX_ca2_e : 0.002564
  EX_cl_e : 0.002564
  EX_cu2_e : 0.000349
  EX_mn2_e : 0.000340
  EX_zn2_e : 0.000168
  EX_ni2_e : 0.000159
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992088
  EX_h2o_e : 547.635228
  EX_co2_e : 27.071335
  EX_ac_e : 3.204816
  Auxiliary production reaction : 0.629582
  EX_ade_e : 0.000332
  EX_glyc__R_e : 0.000165
  DM_5drib_c : 0.000111
  DM_4crsol_c : 0.000110

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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