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 : prlp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (69 of 71: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b1478 b3399 b0474 b2518 b1241 b0351 b2744 b3708 b3008 b0512 b0871 b2925 b2097 b3617 b0160 b2690 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0261 b0822 b2913 b0114 b0509 b3125 b2366 b0755 b3612 b0529 b2492 b0904 b2947 b1533 b3927 b3821 b1380 b2413 b0508 b4042   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.563308 (mmol/gDw/h)
  Minimum Production Rate : 0.127730 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.250848
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.731123
  EX_pi_e : 0.798830
  EX_so4_e : 0.141852
  EX_k_e : 0.109954
  EX_fe2_e : 0.009047
  EX_mg2_e : 0.004887
  EX_ca2_e : 0.002932
  EX_cl_e : 0.002932
  EX_cu2_e : 0.000399
  EX_mn2_e : 0.000389
  EX_zn2_e : 0.000192
  EX_ni2_e : 0.000182
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 46.045770
  EX_co2_e : 26.769249
  EX_h_e : 8.545442
  EX_pyr_e : 2.720530
  Auxiliary production reaction : 0.127730
  EX_alltn_e : 0.002199
  DM_5drib_c : 0.001947
  DM_4crsol_c : 0.001694
  EX_glyclt_e : 0.001569

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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