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 : 2tpr3dpcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (29 of 106: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3399 b4069 b2502 b2744 b3708 b3008 b2297 b2458 b2779 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b1701 b1805 b4381 b2406 b0114 b1539 b2492 b0904 b1533 b3927   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.657914 (mmol/gDw/h)
  Minimum Production Rate : 0.098053 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.980412
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.791794
  EX_pi_e : 1.124895
  EX_so4_e : 0.263729
  EX_k_e : 0.128420
  EX_fe2_e : 0.010567
  EX_mg2_e : 0.005707
  EX_ca2_e : 0.003424
  EX_cl_e : 0.003424
  EX_cu2_e : 0.000466
  EX_mn2_e : 0.000455
  EX_zn2_e : 0.000224
  EX_ni2_e : 0.000213
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 49.013491
  EX_co2_e : 29.482615
  EX_h_e : 6.624316
  EX_ac_e : 0.481082
  Auxiliary production reaction : 0.098053
  DM_5drib_c : 0.000441
  DM_4crsol_c : 0.000147

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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