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 : dhpmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b0871 b2925 b2097 b1851 b2883 b1982 b1200 b3616 b3589 b0675 b2361 b2291 b0261 b0411 b0507 b4381 b0112 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.483531 (mmol/gDw/h)
  Minimum Production Rate : 0.572921 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.887934
  EX_nh4_e : 10.085573
  EX_glc__D_e : 10.000000
  EX_so4_e : 2.130893
  EX_pi_e : 1.039500
  EX_k_e : 0.094382
  EX_fe2_e : 0.007766
  EX_mg2_e : 0.004195
  EX_ca2_e : 0.002517
  EX_cl_e : 0.002517
  EX_cu2_e : 0.000343
  EX_mn2_e : 0.000334
  EX_zn2_e : 0.000165
  EX_ni2_e : 0.000156
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 50.071388
  EX_co2_e : 25.005107
  EX_h_e : 5.288958
  EX_h2s_e : 2.009131
  EX_thymd_e : 0.998761
  Auxiliary production reaction : 0.573083
  DM_oxam_c : 0.000541
  DM_5drib_c : 0.000324
  EX_glyclt_e : 0.000323
  DM_4crsol_c : 0.000108

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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