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 : adpglc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b3553 b4382 b4069 b4384 b0871 b2297 b2458 b2779 b2925 b2097 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b2690 b1982 b4139 b1033 b0261 b2799 b3945 b1602 b2406 b1727 b0114 b0529 b2492 b0904 b3927 b3029 b1380 b2660 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.357126 (mmol/gDw/h)
  Minimum Production Rate : 0.039003 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.050855
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.051951
  EX_pi_e : 0.422493
  EX_so4_e : 0.089932
  EX_k_e : 0.069709
  EX_fe3_e : 0.005736
  EX_mg2_e : 0.003098
  EX_ca2_e : 0.001859
  EX_cl_e : 0.001859
  EX_cu2_e : 0.000253
  EX_mn2_e : 0.000247
  EX_zn2_e : 0.000122
  EX_ni2_e : 0.000115

Product: (mmol/gDw/h)
  EX_h2o_e : 43.407663
  EX_co2_e : 28.000184
  EX_h_e : 9.045660
  EX_pyr_e : 5.433581
  EX_ac_e : 0.207914
  Auxiliary production reaction : 0.039003
  DM_5drib_c : 0.000240
  DM_4crsol_c : 0.000080

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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