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 : cdg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (49 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b3115 b1849 b2296 b2779 b3617 b2883 b1982 b1623 b3665 b0675 b2361 b2291 b0261 b4381 b0112 b4064 b4464 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.482934 (mmol/gDw/h)
  Minimum Production Rate : 0.712954 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.492639
  EX_nh4_e : 10.346367
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.465841
  EX_so4_e : 0.121612
  EX_k_e : 0.094265
  EX_fe2_e : 0.007756
  EX_mg2_e : 0.004189
  EX_ca2_e : 0.002514
  EX_cl_e : 0.002514
  EX_cu2_e : 0.000342
  EX_mn2_e : 0.000334
  EX_zn2_e : 0.000165
  EX_ni2_e : 0.000156
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 48.530581
  EX_co2_e : 21.814073
  EX_h_e : 11.275176
  EX_thymd_e : 1.138105
  EX_ac_e : 0.994111
  Auxiliary production reaction : 0.712954
  EX_ade_e : 0.000540
  DM_5drib_c : 0.000324
  DM_4crsol_c : 0.000108

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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