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 : nadhx__S_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (76 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b3399 b4069 b2502 b4384 b2744 b3708 b3008 b2930 b4232 b3697 b3925 b3115 b1849 b2296 b2779 b2690 b2797 b3117 b1814 b4471 b3665 b4374 b0675 b2361 b2291 b0822 b0112 b3654 b3714 b3664 b1727 b0114 b0529 b1539 b2492 b0904 b3035 b2578 b1533 b3927 b3821 b0789 b1249 b2413 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.586738 (mmol/gDw/h)
  Minimum Production Rate : 0.249285 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.990293
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.081709
  EX_pi_e : 1.064540
  EX_so4_e : 0.147752
  EX_k_e : 0.114527
  EX_fe2_e : 0.009424
  EX_mg2_e : 0.005090
  EX_cl_e : 0.003054
  EX_ca2_e : 0.003054
  EX_cu2_e : 0.000416
  EX_mn2_e : 0.000405
  EX_zn2_e : 0.000200
  EX_ni2_e : 0.000190
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 46.174030
  EX_co2_e : 25.943502
  EX_h_e : 8.330573
  EX_glyc__R_e : 1.351380
  EX_ac_e : 0.341590
  Auxiliary production reaction : 0.249285
  DM_mththf_c : 0.000263
  DM_5drib_c : 0.000132
  DM_4crsol_c : 0.000131

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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