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 : paps_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (31 of 36: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4467 b1478 b3399 b1241 b4069 b4384 b2744 b3115 b1849 b2296 b2926 b0030 b1004 b3713 b1109 b0046 b3236 b1982 b1623 b0261 b2799 b3945 b1602 b4381 b2406 b3915 b0529 b2492 b0904 b1380 b2660 b1695 b0606 b2285 b1007 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.409957 (mmol/gDw/h)
  Minimum Production Rate : 0.549874 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 36.958800
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.222078
  EX_pi_e : 1.495196
  EX_so4_e : 0.653110
  EX_k_e : 0.080021
  EX_fe3_e : 0.006584
  EX_mg2_e : 0.003556
  EX_ca2_e : 0.002134
  EX_cl_e : 0.002134
  EX_cu2_e : 0.000291
  EX_mn2_e : 0.000283
  EX_zn2_e : 0.000140
  EX_ni2_e : 0.000132
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 54.818844
  EX_co2_e : 36.196924
  EX_h_e : 6.178572
  Auxiliary production reaction : 0.549874
  EX_glyclt_e : 0.471640
  EX_ac_e : 0.238671
  EX_hxan_e : 0.010727
  EX_ade_e : 0.000459
  DM_5drib_c : 0.000275
  DM_4crsol_c : 0.000091

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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