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 : accoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (15 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3708 b2297 b2458 b3617 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b0261 b0507 b3709 b2406 b3161 b0112 b0452 b2975 b0114 b3603 b1539 b2492 b0904 b0591 b1533 b1473 b4141 b1798 b3662 b0221   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.437344 (mmol/gDw/h)
  Minimum Production Rate : 0.654349 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.039874
  EX_o2_e : 269.467125
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.304207
  EX_pi_e : 2.384912
  EX_so4_e : 0.764481
  EX_k_e : 0.085366
  EX_mg2_e : 0.003794
  EX_ca2_e : 0.002276
  EX_cl_e : 0.002276
  EX_cu2_e : 0.000310
  EX_mn2_e : 0.000302
  EX_zn2_e : 0.000149
  EX_ni2_e : 0.000141
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992976
  EX_h2o_e : 545.689379
  EX_co2_e : 21.055894
  EX_ac_e : 2.970588
  Auxiliary production reaction : 0.654349
  DM_oxam_c : 0.000489
  DM_5drib_c : 0.000293
  DM_4crsol_c : 0.000098

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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