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 : nadph_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (76 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b2836 b4382 b4069 b4384 b3708 b3008 b2930 b4232 b3697 b3925 b3115 b1849 b2296 b2779 b0030 b2407 b3844 b2690 b1982 b2797 b3117 b1814 b4471 b0261 b3945 b0507 b3709 b2406 b3161 b0112 b2975 b0114 b3603 b0529 b1539 b2492 b0904 b2947 b2578 b1533 b3927 b0594 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.580985 (mmol/gDw/h)
  Minimum Production Rate : 0.244978 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.084069
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.997639
  EX_pi_e : 1.298593
  EX_so4_e : 0.146304
  EX_k_e : 0.113404
  EX_fe2_e : 0.009331
  EX_mg2_e : 0.005040
  EX_ca2_e : 0.003024
  EX_cl_e : 0.003024
  EX_cu2_e : 0.000412
  EX_mn2_e : 0.000401
  EX_zn2_e : 0.000198
  EX_ni2_e : 0.000188
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 46.498814
  EX_co2_e : 25.988107
  EX_h_e : 8.347766
  EX_glyc__R_e : 1.439616
  EX_ac_e : 0.338241
  Auxiliary production reaction : 0.246057
  DM_oxam_c : 0.000650
  DM_5drib_c : 0.000390
  DM_4crsol_c : 0.000130

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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