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 (41 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4382 b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b0871 b2779 b2925 b2097 b0030 b2407 b3236 b0907 b2690 b1982 b3616 b3589 b2210 b0261 b3945 b2406 b0114 b0529 b2492 b0904 b1813 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.289819 (mmol/gDw/h)
  Minimum Production Rate : 0.942392 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.726004
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.015001
  EX_pi_e : 3.106736
  EX_so4_e : 0.072982
  EX_k_e : 0.056571
  EX_fe2_e : 0.004655
  EX_mg2_e : 0.002514
  EX_ca2_e : 0.001509
  EX_cl_e : 0.001509
  EX_cu2_e : 0.000205
  EX_mn2_e : 0.000200
  EX_zn2_e : 0.000099
  EX_ni2_e : 0.000094

Product: (mmol/gDw/h)
  EX_h2o_e : 46.781082
  EX_co2_e : 26.867048
  EX_h_e : 6.442225
  EX_pyr_e : 3.778795
  Auxiliary production reaction : 0.942392
  EX_acald_e : 0.709355
  DM_oxam_c : 0.000195
  DM_5drib_c : 0.000065
  DM_4crsol_c : 0.000065
  EX_glyc__R_e : 0.000065

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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