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 : 4ppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (66 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b3399 b4382 b0586 b0238 b0125 b4069 b4384 b2744 b3708 b3008 b3752 b2297 b2458 b2925 b2097 b2883 b2690 b1982 b0477 b2797 b3117 b1814 b4471 b1623 b3665 b0261 b0411 b3945 b2406 b0114 b1539 b2492 b0904 b2954 b2578 b1533 b3927 b3821 b2413 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.725630 (mmol/gDw/h)
  Minimum Production Rate : 0.030608 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.946829
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.762932
  EX_pi_e : 0.730556
  EX_so4_e : 0.628487
  EX_k_e : 0.141638
  EX_fe2_e : 0.011654
  EX_mg2_e : 0.006295
  EX_ca2_e : 0.003777
  EX_cl_e : 0.003777
  EX_cu2_e : 0.000514
  EX_mn2_e : 0.000501
  EX_zn2_e : 0.000247
  EX_ni2_e : 0.000234
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 47.014711
  EX_co2_e : 25.969838
  EX_h_e : 7.600869
  EX_ac_e : 0.868211
  EX_cgly_e : 0.445759
  Auxiliary production reaction : 0.030608
  EX_ade_e : 0.000812
  DM_5drib_c : 0.000487
  DM_4crsol_c : 0.000162

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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