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 : dnad_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (34 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3399 b1241 b0351 b4069 b4384 b2744 b2297 b2458 b2926 b3617 b0030 b2883 b1982 b1623 b3665 b0261 b0507 b4381 b2406 b0112 b4064 b4464 b0114 b0529 b2492 b0904 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.321969 (mmol/gDw/h)
  Minimum Production Rate : 0.608620 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 32.960336
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.139176
  EX_pi_e : 1.527812
  EX_so4_e : 0.081078
  EX_k_e : 0.062846
  EX_fe2_e : 0.005171
  EX_mg2_e : 0.002793
  EX_ca2_e : 0.001676
  EX_cl_e : 0.001676
  EX_cu2_e : 0.000228
  EX_mn2_e : 0.000222
  EX_zn2_e : 0.000110
  EX_ni2_e : 0.000104

Product: (mmol/gDw/h)
  EX_h2o_e : 52.503132
  EX_co2_e : 31.807992
  EX_h_e : 6.499655
  EX_ac_e : 1.087935
  Auxiliary production reaction : 0.608620
  DM_oxam_c : 0.008425
  EX_ade_e : 0.000360
  DM_5drib_c : 0.000216
  EX_glyclt_e : 0.000215
  DM_4crsol_c : 0.000072

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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