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 : sbzcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (9 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b3553 b4382 b1241 b0351 b4069 b4384 b3708 b3752 b2297 b2458 b3617 b2407 b1982 b2797 b3117 b1814 b4471 b1033 b0596 b4014 b0261 b2976 b0507 b3709 b2406 b3161 b0112 b0452 b0114 b2366 b2492 b0904 b1533 b1473 b4141 b1798 b3662 b0221   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.390254 (mmol/gDw/h)
  Minimum Production Rate : 0.583895 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.577989
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.302413
  EX_pi_e : 2.128126
  EX_so4_e : 0.682169
  EX_k_e : 0.076175
  EX_fe2_e : 0.006268
  EX_mg2_e : 0.003385
  EX_ca2_e : 0.002031
  EX_cl_e : 0.002031
  EX_cu2_e : 0.000277
  EX_mn2_e : 0.000270
  EX_zn2_e : 0.000133
  EX_ni2_e : 0.000126

Product: (mmol/gDw/h)
  EX_h2o_e : 45.481668
  EX_co2_e : 19.993996
  EX_h_e : 8.573006
  EX_ac_e : 2.650481
  Auxiliary production reaction : 0.583895
  DM_oxam_c : 0.000437
  DM_5drib_c : 0.000262
  EX_glyclt_e : 0.000261
  DM_4crsol_c : 0.000087

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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