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 : dcdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b3399 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b0871 b2779 b2925 b2097 b2407 b3236 b3962 b1982 b3616 b3589 b3946 b2210 b0825 b4267 b3665 b0675 b2361 b2799 b4388 b0112 b2789 b3127 b0114 b0509 b3125 b0529 b2492 b0904 b4266 b3662 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.318547 (mmol/gDw/h)
  Minimum Production Rate : 1.035947 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.103286
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.549193
  EX_pi_e : 2.379166
  EX_so4_e : 0.080216
  EX_k_e : 0.062178
  EX_fe2_e : 0.005116
  EX_mg2_e : 0.002763
  EX_ca2_e : 0.001658
  EX_cl_e : 0.001658
  EX_cu2_e : 0.000226
  EX_mn2_e : 0.000220
  EX_zn2_e : 0.000109
  EX_ni2_e : 0.000103

Product: (mmol/gDw/h)
  EX_h2o_e : 47.454671
  EX_co2_e : 26.555501
  EX_h_e : 8.161676
  EX_pyr_e : 3.161561
  Auxiliary production reaction : 1.035947
  EX_acald_e : 0.779597
  EX_ade_e : 0.000214
  EX_glyclt_e : 0.000213
  DM_mththf_c : 0.000143
  DM_5drib_c : 0.000072
  DM_4crsol_c : 0.000071

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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