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 : lald__D_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3553 b3846 b2341 b1241 b0351 b3115 b1849 b2296 b2925 b2097 b1004 b3713 b1109 b0046 b3236 b1779 b2690 b1302 b2662 b1033 b4015 b1602 b2913 b3915 b1727 b1539 b1380 b1771 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.543110 (mmol/gDw/h)
  Minimum Production Rate : 0.180017 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 32.573586
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.865546
  EX_pi_e : 0.523888
  EX_so4_e : 0.136766
  EX_k_e : 0.106011
  EX_fe3_e : 0.008723
  EX_mg2_e : 0.004711
  EX_ca2_e : 0.002827
  EX_cl_e : 0.002827
  EX_cu2_e : 0.000385
  EX_mn2_e : 0.000375
  EX_zn2_e : 0.000185
  EX_ni2_e : 0.000175
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 48.162465
  EX_co2_e : 34.728316
  EX_h_e : 5.315229
  EX_etoh_e : 0.903533
  EX_ac_e : 0.316191
  Auxiliary production reaction : 0.180017
  DM_5drib_c : 0.000122
  DM_4crsol_c : 0.000121

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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