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 : hisp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (76 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b3553 b3399 b3846 b4069 b2744 b2930 b4232 b3697 b3925 b0871 b3115 b1849 b2296 b2926 b0160 b1004 b3713 b1109 b0046 b3236 b1638 b2690 b1982 b4139 b1033 b0675 b2361 b0261 b2799 b3945 b1602 b2913 b4381 b2406 b3915 b1727 b0114 b0529 b2492 b0904 b3029 b1380 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.353832 (mmol/gDw/h)
  Minimum Production Rate : 0.071737 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.032149
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.465540
  EX_pi_e : 0.413045
  EX_so4_e : 0.089102
  EX_k_e : 0.069065
  EX_fe3_e : 0.005683
  EX_mg2_e : 0.003069
  EX_ca2_e : 0.001842
  EX_cl_e : 0.001842
  EX_cu2_e : 0.000251
  EX_mn2_e : 0.000244
  EX_zn2_e : 0.000121
  EX_ni2_e : 0.000114

Product: (mmol/gDw/h)
  EX_h2o_e : 43.465008
  EX_co2_e : 27.922372
  EX_h_e : 9.329366
  EX_pyr_e : 5.294090
  EX_gly_e : 0.390360
  EX_ac_e : 0.205996
  Auxiliary production reaction : 0.071737
  EX_hxan_e : 0.009654
  DM_5drib_c : 0.000237
  DM_4crsol_c : 0.000079

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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