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 : 5mthf_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (90 of 120: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b3553 b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b3708 b3008 b0871 b3617 b0160 b0583 b1982 b2797 b3117 b1814 b4471 b1033 b4374 b0675 b2361 b2291 b4014 b0261 b2976 b0507 b3709 b3161 b0112 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3825 b1473 b0494 b1600 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.393852 (mmol/gDw/h)
  Minimum Production Rate : 0.949260 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.413988
  EX_nh4_e : 10.898810
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.379912
  EX_so4_e : 0.099180
  EX_k_e : 0.076877
  EX_fe2_e : 0.006327
  EX_mg2_e : 0.003417
  EX_ca2_e : 0.002050
  EX_cl_e : 0.002050
  EX_cu2_e : 0.000279
  EX_mn2_e : 0.000272
  EX_zn2_e : 0.000134
  EX_ni2_e : 0.000127

Product: (mmol/gDw/h)
  EX_h2o_e : 47.182205
  EX_co2_e : 19.694150
  EX_h_e : 12.163332
  EX_acald_e : 1.627045
  EX_glyclt_e : 0.949521
  Auxiliary production reaction : 0.949258
  DM_oxam_c : 0.000441
  DM_5drib_c : 0.000264
  DM_4crsol_c : 0.000088

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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