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 : dtdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 70: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b2242 b3553 b0474 b2518 b3831 b2744 b3752 b2781 b1004 b3713 b1109 b0046 b1612 b1611 b4122 b1759 b2210 b1033 b4374 b4161 b2361 b2291 b0411 b4138 b4123 b0621 b0306 b3605 b2492 b0904 b3028 b3821 b3918 b1912 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.565605 (mmol/gDw/h)
  Minimum Production Rate : 0.118065 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.750637
  EX_o2_e : 279.864821
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.789744
  EX_pi_e : 0.781716
  EX_so4_e : 0.142431
  EX_k_e : 0.110402
  EX_mg2_e : 0.004907
  EX_ca2_e : 0.002944
  EX_cl_e : 0.002944
  EX_cu2_e : 0.000401
  EX_mn2_e : 0.000391
  EX_zn2_e : 0.000193
  EX_ni2_e : 0.000183
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.930823
  EX_h2o_e : 549.121782
  EX_co2_e : 30.791953
  EX_succ_e : 0.589809
  Auxiliary production reaction : 0.118065
  EX_ura_e : 0.102376
  EX_pheme_e : 0.060093
  DM_5drib_c : 0.000127
  DM_4crsol_c : 0.000126

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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