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 : his__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 76: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b4382 b4384 b3708 b3008 b0910 b3752 b0871 b2925 b2097 b2926 b2407 b2690 b1982 b2797 b3117 b1814 b4471 b0596 b0261 b3945 b2239 b2406 b0112 b3453 b2868 b0114 b0886 b0529 b1539 b2492 b0904 b2578 b1533 b3927 b2835 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.615614 (mmol/gDw/h)
  Minimum Production Rate : 0.423916 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.151702
  EX_o2_e : 276.526069
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.923775
  EX_pi_e : 0.593825
  EX_so4_e : 0.155024
  EX_k_e : 0.120164
  EX_mg2_e : 0.005340
  EX_ca2_e : 0.003204
  EX_cl_e : 0.003204
  EX_cu2_e : 0.000436
  EX_mn2_e : 0.000425
  EX_zn2_e : 0.000210
  EX_ni2_e : 0.000199
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990113
  EX_h2o_e : 547.172243
  EX_co2_e : 26.463420
  EX_pyr_e : 1.906708
  Auxiliary production reaction : 0.423916
  EX_ade_e : 0.000689
  DM_5drib_c : 0.000413
  DM_4crsol_c : 0.000137

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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