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 : dutp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3553 b4382 b4069 b4384 b2297 b2458 b2779 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1982 b1033 b0261 b2799 b3945 b1602 b2913 b2406 b3915 b1727 b0114 b0529 b2492 b0904 b3927 b1380 b3662 b0606 b2285 b1010 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.452390 (mmol/gDw/h)
  Minimum Production Rate : 0.480784 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.088835
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.849875
  EX_pi_e : 1.878730
  EX_so4_e : 0.113921
  EX_k_e : 0.088303
  EX_fe3_e : 0.007266
  EX_mg2_e : 0.003924
  EX_ca2_e : 0.002355
  EX_cl_e : 0.002355
  EX_cu2_e : 0.000321
  EX_mn2_e : 0.000313
  EX_zn2_e : 0.000154
  EX_ni2_e : 0.000146
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.848973
  EX_co2_e : 36.574113
  EX_h_e : 4.429914
  Auxiliary production reaction : 0.480784
  EX_ac_e : 0.263375
  EX_ade_e : 0.000506
  DM_5drib_c : 0.000304
  DM_4crsol_c : 0.000101

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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