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 : preq1_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (84 of 95: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b3553 b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b3752 b0871 b2779 b0160 b2883 b0907 b1779 b1982 b3616 b3589 b1033 b1623 b4374 b2361 b2291 b0261 b0411 b0112 b2789 b3127 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.407662 (mmol/gDw/h)
  Minimum Production Rate : 1.325211 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.648881
  EX_nh4_e : 11.029221
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.393233
  EX_so4_e : 0.102657
  EX_k_e : 0.079573
  EX_fe2_e : 0.006547
  EX_mg2_e : 0.003536
  EX_ca2_e : 0.002122
  EX_cl_e : 0.002122
  EX_cu2_e : 0.000289
  EX_mn2_e : 0.000282
  EX_zn2_e : 0.000139
  EX_ni2_e : 0.000132
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 50.710165
  EX_co2_e : 26.691927
  EX_h_e : 9.047695
  EX_acald_e : 3.648387
  Auxiliary production reaction : 1.325211
  DM_oxam_c : 0.000456
  DM_5drib_c : 0.000274
  EX_glyclt_e : 0.000182
  DM_4crsol_c : 0.000091

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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