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 : grdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (44 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b4467 b1478 b4269 b0493 b3588 b3003 b3011 b0474 b2518 b1241 b0871 b2926 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1638 b0261 b2799 b3945 b1602 b3915 b2492 b0904 b3029 b1380 b2660 b1695 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.484185 (mmol/gDw/h)
  Minimum Production Rate : 0.029487 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.163834
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.229153
  EX_pi_e : 0.526004
  EX_so4_e : 0.121928
  EX_k_e : 0.094509
  EX_fe3_e : 0.007778
  EX_mg2_e : 0.004200
  EX_ca2_e : 0.002520
  EX_cl_e : 0.002520
  EX_cu2_e : 0.000343
  EX_mn2_e : 0.000335
  EX_zn2_e : 0.000165
  EX_ni2_e : 0.000156
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 51.692379
  EX_co2_e : 37.812049
  EX_h_e : 5.436990
  EX_fum_e : 0.504904
  Auxiliary production reaction : 0.029478
  DM_5drib_c : 0.000109
  DM_4crsol_c : 0.000108

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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