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 : q8_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (69 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b4069 b4384 b3708 b3752 b2297 b2458 b2779 b2925 b2097 b2407 b1612 b1611 b4122 b2690 b1982 b2797 b3117 b1814 b4471 b2440 b3945 b4381 b2406 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.597835 (mmol/gDw/h)
  Minimum Production Rate : 0.038040 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.662727
  EX_o2_e : 276.427890
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.571084
  EX_pi_e : 0.576675
  EX_so4_e : 0.150547
  EX_k_e : 0.116693
  EX_mg2_e : 0.005186
  EX_ca2_e : 0.003112
  EX_cl_e : 0.003112
  EX_cu2_e : 0.000424
  EX_mn2_e : 0.000413
  EX_zn2_e : 0.000204
  EX_ni2_e : 0.000193
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990398
  EX_h2o_e : 545.206028
  EX_co2_e : 27.033235
  EX_fum_e : 0.852459
  EX_glyc__R_e : 0.552517
  EX_ac_e : 0.348051
  DM_oxam_c : 0.114521
  DM_mththf_c : 0.114386
  Auxiliary production reaction : 0.038040
  DM_5drib_c : 0.000135
  DM_4crsol_c : 0.000133

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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