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 : nadph_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (69 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4467 b1478 b4382 b1241 b4069 b4384 b3752 b2297 b2458 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b1982 b0477 b4139 b0261 b2799 b3945 b1602 b2913 b2406 b3915 b0114 b0529 b1539 b2492 b0904 b2954 b3029 b1380 b3662 b0221 b2285 b1008   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.438236 (mmol/gDw/h)
  Minimum Production Rate : 0.186617 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.777568
  EX_o2_e : 287.110981
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.039226
  EX_pi_e : 0.982575
  EX_so4_e : 0.110357
  EX_k_e : 0.085541
  EX_mg2_e : 0.003802
  EX_cl_e : 0.002281
  EX_ca2_e : 0.002281
  EX_cu2_e : 0.000311
  EX_mn2_e : 0.000303
  EX_zn2_e : 0.000149
  EX_ni2_e : 0.000142
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992961
  EX_h2o_e : 553.069282
  EX_co2_e : 37.581256
  EX_ac_e : 0.255135
  Auxiliary production reaction : 0.186617
  EX_glyclt_e : 0.000490
  DM_5drib_c : 0.000294
  DM_4crsol_c : 0.000098

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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