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 : dadp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (91 of 95: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b3553 b4382 b0238 b0125 b1241 b0351 b4384 b0871 b2925 b2097 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b2883 b2690 b0477 b1033 b0411 b2799 b3945 b1602 b3915 b2868 b1727 b4064 b4464 b0529 b2492 b0904 b1380 b2660 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.379887 (mmol/gDw/h)
  Minimum Production Rate : 0.010275 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.165575
  EX_o2_e : 279.953120
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.155399
  EX_pi_e : 0.386992
  EX_so4_e : 0.095663
  EX_k_e : 0.074151
  EX_mg2_e : 0.003296
  EX_ca2_e : 0.001977
  EX_cl_e : 0.001977
  EX_cu2_e : 0.000269
  EX_mn2_e : 0.000263
  EX_zn2_e : 0.000130
  EX_ni2_e : 0.000123

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993899
  EX_h2o_e : 543.056681
  EX_co2_e : 29.536691
  EX_pyr_e : 4.295393
  EX_etoh_e : 0.940247
  Auxiliary production reaction : 0.010275
  EX_ade_e : 0.000256
  DM_5drib_c : 0.000085
  DM_4crsol_c : 0.000085

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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