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 : imacp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (35 of 103: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b1241 b0351 b4069 b2502 b2744 b3115 b1849 b2296 b3616 b3589 b1623 b3665 b0675 b2361 b4381 b2406 b0112 b3654 b3714 b3664 b0114 b0529 b2492 b0904 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.562719 (mmol/gDw/h)
  Minimum Production Rate : 2.128934 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 22.317556
  EX_nh4_e : 10.335180
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.671735
  EX_so4_e : 0.141704
  EX_k_e : 0.109839
  EX_fe2_e : 0.009038
  EX_mg2_e : 0.004882
  EX_ca2_e : 0.002929
  EX_cl_e : 0.002929
  EX_cu2_e : 0.000399
  EX_mn2_e : 0.000389
  EX_zn2_e : 0.000192
  EX_ni2_e : 0.000182
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 50.087386
  EX_co2_e : 22.453942
  EX_h_e : 10.265442
  Auxiliary production reaction : 2.128934
  EX_ac_e : 0.837092
  EX_mththf_e : 0.000252
  DM_5drib_c : 0.000127
  DM_4crsol_c : 0.000125

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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