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 : bmoco1gdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 137: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3399 b2744 b3708 b3008 b0871 b0160 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b4381 b2406 b0452 b2868 b0114 b2366 b2492 b0904 b2947 b2578 b1533 b3927 b1511 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.783007 (mmol/gDw/h)
  Minimum Production Rate : 0.028161 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.327975
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.963409
  EX_pi_e : 0.839776
  EX_so4_e : 0.309821
  EX_k_e : 0.152837
  EX_mobd_e : 0.028167
  EX_mg2_e : 0.006793
  EX_fe2_e : 0.006462
  EX_fe3_e : 0.006114
  EX_ca2_e : 0.004076
  EX_cl_e : 0.004076
  EX_cu2_e : 0.000555
  EX_mn2_e : 0.000541
  EX_zn2_e : 0.000267
  EX_ni2_e : 0.000253
  EX_cobalt2_e : 0.000020

Product: (mmol/gDw/h)
  EX_h2o_e : 49.012247
  EX_co2_e : 26.909512
  EX_h_e : 7.369762
  Auxiliary production reaction : 0.028161
  EX_xan_e : 0.020488
  EX_ade_e : 0.000527
  DM_mththf_c : 0.000351
  DM_5drib_c : 0.000176
  DM_4crsol_c : 0.000175

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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