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 (48 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b3553 b3399 b4069 b2502 b2744 b2297 b2458 b3844 b1004 b3713 b1109 b0046 b3236 b0937 b1982 b1033 b0675 b2361 b0261 b2799 b3945 b1602 b2913 b4381 b2406 b1727 b0114 b0755 b3612 b0529 b2492 b0904 b3927 b1380 b0514 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.390674 (mmol/gDw/h)
  Minimum Production Rate : 0.859324 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.726506
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.850513
  EX_pi_e : 2.954818
  EX_so4_e : 0.098379
  EX_k_e : 0.076257
  EX_fe2_e : 0.006275
  EX_mg2_e : 0.003389
  EX_ca2_e : 0.002033
  EX_cl_e : 0.002033
  EX_cu2_e : 0.000277
  EX_mn2_e : 0.000270
  EX_zn2_e : 0.000133
  EX_ni2_e : 0.000126

Product: (mmol/gDw/h)
  EX_h2o_e : 53.690776
  EX_co2_e : 35.023438
  EX_h_e : 4.729733
  Auxiliary production reaction : 0.859324
  EX_etoh_e : 0.349112
  EX_ac_e : 0.227445
  EX_ade_e : 0.010660
  DM_5drib_c : 0.000262
  DM_4crsol_c : 0.000087

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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