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 : glyc__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b2836 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3708 b3008 b3752 b0871 b2779 b2926 b2407 b1238 b0121 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b0261 b4381 b2406 b0112 b2789 b3127 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.494987 (mmol/gDw/h)
  Minimum Production Rate : 0.298244 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.609162
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.942899
  EX_pi_e : 0.477467
  EX_so4_e : 0.124648
  EX_k_e : 0.096618
  EX_fe2_e : 0.007950
  EX_mg2_e : 0.004294
  EX_ca2_e : 0.002576
  EX_cl_e : 0.002576
  EX_cu2_e : 0.000351
  EX_mn2_e : 0.000342
  EX_zn2_e : 0.000169
  EX_ni2_e : 0.000160
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 43.592777
  EX_co2_e : 27.537993
  EX_h_e : 6.040630
  EX_acald_e : 1.448360
  DM_oxam_c : 0.597041
  DM_5drib_c : 0.596820
  DM_4crsol_c : 0.596598
  Auxiliary production reaction : 0.298409
  EX_etha_e : 0.000040

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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