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 : pe181_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (69 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b1054 b2836 b0474 b2518 b2744 b4152 b2781 b3844 b1612 b1611 b4122 b1759 b4374 b4161 b0675 b4138 b4123 b0621 b4381 b2406 b3915 b2197 b3918 b0789 b1249 b1695 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.545568 (mmol/gDw/h)
  Minimum Production Rate : 0.287336 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 17.091092
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.953201
  EX_pi_e : 0.813594
  EX_so4_e : 0.137385
  EX_k_e : 0.106491
  EX_fe3_e : 0.008762
  EX_mg2_e : 0.004733
  EX_ca2_e : 0.002840
  EX_cl_e : 0.002840
  EX_cu2_e : 0.000387
  EX_mn2_e : 0.000377
  EX_zn2_e : 0.000186
  EX_ni2_e : 0.000176
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 40.335926
  EX_co2_e : 21.993329
  EX_h_e : 6.647536
  EX_succ_e : 0.568914
  EX_ura_e : 0.386888
  Auxiliary production reaction : 0.287336
  EX_hxa_e : 0.001607
  DM_5drib_c : 0.000123
  DM_4crsol_c : 0.000122

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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