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 : dudp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (45 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b0586 b4384 b3708 b3008 b3752 b0871 b2407 b1238 b2797 b3117 b1814 b4471 b3665 b3709 b4381 b2406 b3161 b0112 b3654 b3714 b3664 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b3821 b1473 b4141 b1798 b3662 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.743853 (mmol/gDw/h)
  Minimum Production Rate : 0.515052 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.758755
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.063657
  EX_pi_e : 1.747630
  EX_so4_e : 0.187317
  EX_k_e : 0.145195
  EX_fe2_e : 0.011947
  EX_mg2_e : 0.006453
  EX_ca2_e : 0.003872
  EX_cl_e : 0.003872
  EX_cu2_e : 0.000527
  EX_mn2_e : 0.000514
  EX_zn2_e : 0.000254
  EX_ni2_e : 0.000240
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.594629
  EX_co2_e : 24.831101
  EX_h_e : 7.349874
  Auxiliary production reaction : 0.515052
  DM_mththf_c : 0.000333
  DM_5drib_c : 0.000167
  DM_4crsol_c : 0.000166

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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