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 : 4r5au_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (52 of 111: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b2744 b2297 b2458 b2779 b0030 b2407 b0907 b1779 b1982 b3616 b3589 b0261 b0411 b0112 b2789 b3127 b2975 b0114 b3603 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.395346 (mmol/gDw/h)
  Minimum Production Rate : 1.515340 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.893190
  EX_nh4_e : 10.331503
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.381353
  EX_so4_e : 0.099556
  EX_k_e : 0.077169
  EX_fe2_e : 0.006350
  EX_mg2_e : 0.003430
  EX_ca2_e : 0.002058
  EX_cl_e : 0.002058
  EX_cu2_e : 0.000280
  EX_mn2_e : 0.000273
  EX_zn2_e : 0.000135
  EX_ni2_e : 0.000128

Product: (mmol/gDw/h)
  EX_h2o_e : 45.753777
  EX_co2_e : 24.705523
  EX_h_e : 12.408336
  EX_ac_e : 2.713320
  Auxiliary production reaction : 1.515340
  DM_oxam_c : 0.000442
  DM_5drib_c : 0.000265
  EX_dxylnt_e : 0.000176
  DM_4crsol_c : 0.000088

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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