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 : dctp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b3553 b1478 b3399 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b2502 b4384 b2744 b0871 b2779 b0030 b3844 b1004 b3713 b1109 b0046 b3236 b0937 b1982 b1033 b1623 b2361 b2291 b0261 b2799 b3945 b1602 b2406 b0509 b3125 b0529 b2492 b0904 b1380 b2660 b0606 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.375586 (mmol/gDw/h)
  Minimum Production Rate : 0.962761 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.424772
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.946682
  EX_pi_e : 3.250575
  EX_so4_e : 0.094580
  EX_k_e : 0.073312
  EX_fe2_e : 0.006032
  EX_mg2_e : 0.003258
  EX_ca2_e : 0.001955
  EX_cl_e : 0.001955
  EX_cu2_e : 0.000266
  EX_mn2_e : 0.000260
  EX_zn2_e : 0.000128
  EX_ni2_e : 0.000121

Product: (mmol/gDw/h)
  EX_h2o_e : 54.143269
  EX_co2_e : 34.593268
  EX_h_e : 4.415897
  Auxiliary production reaction : 0.962761
  EX_acald_e : 0.661431
  EX_ade_e : 0.000420
  DM_5drib_c : 0.000252
  DM_4crsol_c : 0.000084

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.

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Last updated: 21-Sep-2023
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