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 : ppgpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b2744 b3708 b3008 b0871 b2925 b2097 b2883 b2690 b2797 b3117 b1814 b4471 b3945 b4381 b2406 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b3825 b0494 b3662 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.778419 (mmol/gDw/h)
  Minimum Production Rate : 0.118473 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.822990
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.305169
  EX_pi_e : 1.469515
  EX_so4_e : 0.196021
  EX_k_e : 0.151942
  EX_fe2_e : 0.012502
  EX_mg2_e : 0.006753
  EX_ca2_e : 0.004052
  EX_cl_e : 0.004052
  EX_cu2_e : 0.000552
  EX_mn2_e : 0.000538
  EX_zn2_e : 0.000265
  EX_ni2_e : 0.000251
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 49.257179
  EX_co2_e : 25.883977
  EX_h_e : 7.813789
  Auxiliary production reaction : 0.179662
  EX_pyr_e : 0.122378
  EX_mththf_e : 0.000349
  DM_5drib_c : 0.000175
  DM_4crsol_c : 0.000174

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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