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 : adpglc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b3553 b4269 b0493 b3588 b3003 b3011 b4384 b0871 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b1033 b0261 b2799 b3945 b1602 b0153 b2913 b4381 b0590 b2406 b1727 b0114 b0755 b3612 b0529 b2492 b0904 b1380 b3662 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.434104 (mmol/gDw/h)
  Minimum Production Rate : 0.292208 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 35.723531
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.151265
  EX_pi_e : 1.003155
  EX_so4_e : 0.109316
  EX_k_e : 0.084734
  EX_fe2_e : 0.006972
  EX_mg2_e : 0.003766
  EX_ca2_e : 0.002260
  EX_cl_e : 0.002260
  EX_cu2_e : 0.000308
  EX_mn2_e : 0.000300
  EX_zn2_e : 0.000148
  EX_ni2_e : 0.000140
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 51.477038
  EX_co2_e : 36.446626
  EX_h_e : 4.867284
  EX_etoh_e : 0.528346
  Auxiliary production reaction : 0.292208
  EX_hxan_e : 0.000486
  DM_5drib_c : 0.000291
  DM_4crsol_c : 0.000097

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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