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 : dump_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (77 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b1479 b0871 b2925 b2097 b0030 b2407 b3844 b3236 b1779 b2690 b2463 b3962 b3616 b3589 b2210 b4267 b3665 b1415 b3551 b3945 b4388 b4219 b1832 b1778 b4381 b0112 b0114 b0529 b2492 b0904 b1380 b0325 b1710 b2480 b0508 b4266 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.287975 (mmol/gDw/h)
  Minimum Production Rate : 0.760959 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.765084
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.984127
  EX_pi_e : 1.214307
  EX_so4_e : 0.072518
  EX_k_e : 0.056211
  EX_fe2_e : 0.004625
  EX_mg2_e : 0.002498
  EX_ca2_e : 0.001499
  EX_cl_e : 0.001499
  EX_cu2_e : 0.000204
  EX_mn2_e : 0.000199
  EX_zn2_e : 0.000098
  EX_ni2_e : 0.000093

Product: (mmol/gDw/h)
  EX_h2o_e : 44.865987
  EX_co2_e : 26.886077
  EX_h_e : 8.337912
  EX_pyr_e : 3.817669
  Auxiliary production reaction : 0.936525
  EX_acald_e : 0.704777
  EX_ade_e : 0.000194
  EX_dxylnt_e : 0.000193
  EX_mththf_e : 0.000129
  DM_5drib_c : 0.000065
  DM_4crsol_c : 0.000064

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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