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 (49 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b3553 b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b3926 b0871 b2926 b3617 b1004 b3713 b1109 b0046 b3236 b2883 b1982 b1033 b0675 b2361 b2291 b0261 b0411 b1602 b4381 b0114 b0529 b2492 b0904 b1380 b2660 b3662 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.386383 (mmol/gDw/h)
  Minimum Production Rate : 0.529939 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 34.421395
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.942744
  EX_pi_e : 1.432586
  EX_so4_e : 0.097299
  EX_k_e : 0.075419
  EX_fe3_e : 0.006206
  EX_mg2_e : 0.003352
  EX_ca2_e : 0.002011
  EX_cl_e : 0.002011
  EX_cu2_e : 0.000274
  EX_mn2_e : 0.000267
  EX_zn2_e : 0.000132
  EX_ni2_e : 0.000125

Product: (mmol/gDw/h)
  EX_h2o_e : 53.320595
  EX_co2_e : 34.330874
  EX_h_e : 6.796348
  EX_his__L_e : 0.726099
  Auxiliary production reaction : 0.529939
  EX_etoh_e : 0.340411
  EX_hxan_e : 0.000432
  DM_5drib_c : 0.000259
  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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