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 : 2h3oppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (76 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b3553 b1478 b3399 b1241 b4069 b2744 b2297 b2458 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b0937 b1982 b4139 b1033 b0675 b2361 b2291 b4014 b0261 b2976 b2799 b3945 b1602 b4381 b0509 b3125 b0529 b2492 b0904 b2954 b3029 b1380 b2660 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.458802 (mmol/gDw/h)
  Minimum Production Rate : 0.234279 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 39.131798
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.008911
  EX_pi_e : 0.442563
  EX_so4_e : 0.115535
  EX_k_e : 0.089555
  EX_mg2_e : 0.003980
  EX_fe2_e : 0.003786
  EX_fe3_e : 0.003582
  EX_ca2_e : 0.002388
  EX_cl_e : 0.002388
  EX_cu2_e : 0.000325
  EX_mn2_e : 0.000317
  EX_zn2_e : 0.000156
  EX_ni2_e : 0.000148
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.255298
  EX_co2_e : 39.850665
  EX_h_e : 4.800175
  EX_ac_e : 0.292769
  Auxiliary production reaction : 0.234279
  EX_urea_e : 0.025661
  EX_ade_e : 0.000513
  DM_5drib_c : 0.000308
  DM_4crsol_c : 0.000102

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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