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 : succoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (16 of 28: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b0945 b4382 b1241 b0351 b4069 b4384 b3708 b2297 b2458 b0030 b2407 b3124 b1779 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b0261 b1701 b1805 b2406 b0112 b2868 b0114 b0755 b3612 b1539 b2492 b0904 b1533 b0723 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.453289 (mmol/gDw/h)
  Minimum Production Rate : 0.149901 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.660859
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.214109
  EX_pi_e : 0.886950
  EX_so4_e : 0.264049
  EX_k_e : 0.088479
  EX_fe2_e : 0.007280
  EX_mg2_e : 0.003932
  EX_ca2_e : 0.002359
  EX_cl_e : 0.002359
  EX_cu2_e : 0.000321
  EX_mn2_e : 0.000313
  EX_zn2_e : 0.000155
  EX_ni2_e : 0.000146
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 46.378619
  EX_co2_e : 25.361880
  EX_h_e : 9.207783
  EX_ac_e : 1.947033
  EX_ade_e : 0.453862
  DM_5drib_c : 0.453659
  DM_4crsol_c : 0.453456
  EX_glyc__R_e : 0.226829
  Auxiliary production reaction : 0.149901

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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