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 : duri_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (23 of 50: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b2066 b1241 b0351 b0910 b0871 b2779 b2925 b2097 b3617 b0030 b2407 b1238 b0907 b2498 b3946 b0825 b4381 b2868 b0114 b2492 b0904 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.566431 (mmol/gDw/h)
  Minimum Production Rate : 0.102526 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.873007
  EX_o2_e : 276.384527
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.915269
  EX_pi_e : 0.546383
  EX_so4_e : 0.142639
  EX_k_e : 0.110563
  EX_mg2_e : 0.004914
  EX_cl_e : 0.002948
  EX_ca2_e : 0.002948
  EX_cu2_e : 0.000402
  EX_mn2_e : 0.000391
  EX_zn2_e : 0.000193
  EX_ni2_e : 0.000183
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990903
  EX_h2o_e : 547.461013
  EX_co2_e : 26.058705
  EX_acald_e : 1.590279
  EX_glyc__R_e : 1.115440
  EX_hxan_e : 0.545676
  Auxiliary production reaction : 0.102526
  EX_xan_e : 0.102526
  DM_mththf_c : 0.000254
  DM_5drib_c : 0.000127
  DM_4crsol_c : 0.000126

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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