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 : forcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (23 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3399 b1241 b0351 b2744 b3708 b3008 b0871 b2925 b2097 b3617 b0160 b2690 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0261 b3945 b0114 b1539 b2492 b0904 b1533 b3927 b3825 b0494   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.772889 (mmol/gDw/h)
  Minimum Production Rate : 0.076031 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.746179
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.880211
  EX_pi_e : 0.973625
  EX_so4_e : 0.270660
  EX_k_e : 0.150862
  EX_fe2_e : 0.012413
  EX_mg2_e : 0.006705
  EX_ca2_e : 0.004023
  EX_cl_e : 0.004023
  EX_cu2_e : 0.000548
  EX_mn2_e : 0.000534
  EX_zn2_e : 0.000264
  EX_ni2_e : 0.000250
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.398207
  EX_co2_e : 26.398846
  EX_h_e : 7.398597
  Auxiliary production reaction : 0.076031
  EX_pyr_e : 0.067167
  DM_oxam_c : 0.000865
  DM_5drib_c : 0.000519
  DM_4crsol_c : 0.000172

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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