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 : cpmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (36 of 38: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b3553 b4069 b4384 b3752 b0871 b2297 b2458 b2925 b2097 b2926 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b3908 b1656 b1982 b4139 b3946 b0825 b1033 b0261 b2799 b3945 b1602 b2913 b4381 b2406 b1727 b0114 b0529 b2492 b0904 b3927 b1380 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.357729 (mmol/gDw/h)
  Minimum Production Rate : 0.062272 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.182817
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.174802
  EX_pi_e : 0.407340
  EX_so4_e : 0.090083
  EX_k_e : 0.069826
  EX_fe2_e : 0.005745
  EX_mg2_e : 0.003103
  EX_ca2_e : 0.001862
  EX_cl_e : 0.001862
  EX_cu2_e : 0.000254
  EX_mn2_e : 0.000247
  EX_zn2_e : 0.000122
  EX_ni2_e : 0.000116

Product: (mmol/gDw/h)
  EX_h2o_e : 43.656844
  EX_co2_e : 28.056010
  EX_h_e : 9.151248
  EX_pyr_e : 5.406939
  EX_ac_e : 0.208265
  Auxiliary production reaction : 0.062272
  DM_5drib_c : 0.000240
  DM_4crsol_c : 0.000080

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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