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 : aacoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (22 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b3553 b3399 b4069 b2502 b2744 b3708 b3008 b3115 b1849 b2296 b0583 b1982 b2797 b3117 b1814 b4471 b1033 b4374 b0675 b2361 b2291 b4014 b0261 b2976 b0507 b3709 b3161 b0112 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b3821 b1473 b1600 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.664852 (mmol/gDw/h)
  Minimum Production Rate : 0.067878 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.592193
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.579999
  EX_pi_e : 1.272457
  EX_so4_e : 0.235301
  EX_k_e : 0.129774
  EX_fe2_e : 0.010678
  EX_mg2_e : 0.005768
  EX_ca2_e : 0.003461
  EX_cl_e : 0.003461
  EX_cu2_e : 0.000471
  EX_mn2_e : 0.000459
  EX_zn2_e : 0.000227
  EX_ni2_e : 0.000215
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 49.084900
  EX_co2_e : 24.329779
  EX_h_e : 8.265254
  EX_ac_e : 0.454945
  EX_fad_e : 0.213752
  Auxiliary production reaction : 0.067878
  DM_oxam_c : 0.000744
  DM_5drib_c : 0.000446
  DM_4crsol_c : 0.000148

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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