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 : datp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (92 of 114: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b2066 b1241 b0351 b4069 b4384 b3752 b2930 b4232 b3697 b3925 b2297 b2458 b2926 b2407 b2690 b3962 b4139 b2498 b3616 b3589 b4267 b1415 b0261 b3945 b2868 b0114 b0529 b2492 b0904 b1380 b0325 b0508 b4266   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.356750 (mmol/gDw/h)
  Minimum Production Rate : 0.263454 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 31.347833
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.326069
  EX_pi_e : 1.134486
  EX_so4_e : 0.089837
  EX_k_e : 0.069635
  EX_fe2_e : 0.005730
  EX_mg2_e : 0.003095
  EX_ca2_e : 0.001857
  EX_cl_e : 0.001857
  EX_cu2_e : 0.000253
  EX_mn2_e : 0.000247
  EX_zn2_e : 0.000122
  EX_ni2_e : 0.000115

Product: (mmol/gDw/h)
  EX_h2o_e : 47.002517
  EX_co2_e : 31.004157
  EX_h_e : 9.639056
  EX_ac_e : 4.414566
  EX_thym_e : 0.577361
  Auxiliary production reaction : 0.263454
  EX_ade_e : 0.000240
  EX_dxylnt_e : 0.000239
  DM_5drib_c : 0.000080
  DM_4crsol_c : 0.000080

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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