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 : duri_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (38 of 50: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b3553 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b2930 b4232 b3697 b3925 b0871 b3617 b0030 b2407 b1004 b3713 b1109 b0046 b0907 b2690 b1982 b2210 b1033 b0411 b3945 b0114 b0529 b2492 b0904 b1380 b0515 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.384436 (mmol/gDw/h)
  Minimum Production Rate : 1.250225 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.677094
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.653363
  EX_pi_e : 0.370829
  EX_so4_e : 0.096809
  EX_k_e : 0.075039
  EX_fe2_e : 0.006174
  EX_mg2_e : 0.003335
  EX_ca2_e : 0.002001
  EX_cl_e : 0.002001
  EX_cu2_e : 0.000273
  EX_mn2_e : 0.000266
  EX_zn2_e : 0.000131
  EX_ni2_e : 0.000124

Product: (mmol/gDw/h)
  EX_h2o_e : 45.245596
  EX_co2_e : 25.843375
  EX_h_e : 7.781001
  EX_pyr_e : 1.747163
  Auxiliary production reaction : 1.250225
  EX_acald_e : 0.940937
  EX_alltn_e : 0.000259
  DM_mththf_c : 0.000172
  DM_5drib_c : 0.000086
  DM_4crsol_c : 0.000086

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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