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 : aps_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b4467 b4382 b4269 b0493 b3588 b3003 b3011 b3831 b4384 b0871 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b0937 b1982 b0261 b0411 b3945 b1602 b1727 b0114 b0529 b2492 b0904 b1380 b2660 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.462958 (mmol/gDw/h)
  Minimum Production Rate : 0.123809 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.895146
  EX_o2_e : 287.668203
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.621547
  EX_pi_e : 0.570382
  EX_so4_e : 0.240391
  EX_k_e : 0.090366
  EX_mg2_e : 0.004016
  EX_ca2_e : 0.002410
  EX_cl_e : 0.002410
  EX_cu2_e : 0.000328
  EX_mn2_e : 0.000320
  EX_zn2_e : 0.000158
  EX_ni2_e : 0.000150
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992564
  EX_h2o_e : 552.183742
  EX_co2_e : 38.347310
  EX_3hpp_e : 0.469554
  Auxiliary production reaction : 0.123809
  EX_ade_e : 0.000518
  DM_5drib_c : 0.000311
  DM_4crsol_c : 0.000103

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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