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 : prlp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (58 of 71: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4467 b1478 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b4384 b3752 b0871 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b1982 b0261 b0411 b2799 b3945 b1602 b2913 b3915 b0529 b2492 b0904 b1380 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.384820 (mmol/gDw/h)
  Minimum Production Rate : 0.491671 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 35.484823
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.616532
  EX_pi_e : 1.354541
  EX_so4_e : 0.096905
  EX_k_e : 0.075114
  EX_fe3_e : 0.006181
  EX_mg2_e : 0.003338
  EX_cl_e : 0.002003
  EX_ca2_e : 0.002003
  EX_cu2_e : 0.000273
  EX_mn2_e : 0.000266
  EX_zn2_e : 0.000131
  EX_ni2_e : 0.000124

Product: (mmol/gDw/h)
  EX_h2o_e : 51.049252
  EX_co2_e : 34.494279
  EX_h_e : 7.168842
  EX_glyclt_e : 1.166273
  Auxiliary production reaction : 0.491671
  EX_ade_e : 0.000431
  DM_5drib_c : 0.000258
  DM_4crsol_c : 0.000086

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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