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 : adphep_DD_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (39 of 99: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b3115 b1849 b2296 b2926 b3617 b2883 b1982 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 : 0.469525 (mmol/gDw/h)
  Minimum Production Rate : 0.462106 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.160963
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.132272
  EX_pi_e : 1.377119
  EX_so4_e : 0.118236
  EX_k_e : 0.091648
  EX_fe2_e : 0.007541
  EX_mg2_e : 0.004073
  EX_ca2_e : 0.002444
  EX_cl_e : 0.002444
  EX_cu2_e : 0.000333
  EX_mn2_e : 0.000324
  EX_zn2_e : 0.000160
  EX_ni2_e : 0.000152
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 47.691125
  EX_co2_e : 23.570052
  EX_h_e : 7.724763
  EX_thymd_e : 0.875454
  Auxiliary production reaction : 0.462106
  EX_ac_e : 0.273351
  DM_5drib_c : 0.000315
  DM_4crsol_c : 0.000105

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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