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 : dcyt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (18 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4382 b0474 b2518 b1241 b0351 b4069 b4384 b2744 b3752 b2297 b2458 b2781 b0099 b3617 b0160 b2883 b1982 b1623 b0261 b2406 b0112 b2868 b4064 b4464 b0114 b0529 b2492 b0904 b2954 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.507817 (mmol/gDw/h)
  Minimum Production Rate : 1.946435 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.013217
  EX_nh4_e : 11.326523
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.489843
  EX_so4_e : 0.127878
  EX_k_e : 0.099122
  EX_fe2_e : 0.008156
  EX_mg2_e : 0.004405
  EX_ca2_e : 0.002643
  EX_cl_e : 0.002643
  EX_cu2_e : 0.000360
  EX_mn2_e : 0.000351
  EX_zn2_e : 0.000173
  EX_ni2_e : 0.000164
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 47.189928
  EX_co2_e : 20.149167
  EX_h_e : 11.250870
  Auxiliary production reaction : 1.946435
  EX_ac_e : 0.742701
  EX_ade_e : 0.000568
  DM_5drib_c : 0.000341
  DM_4crsol_c : 0.000113

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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