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 : glyclt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (53 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b4382 b4069 b4384 b3708 b3008 b2297 b2458 b0030 b2407 b1982 b2688 b2797 b3117 b1814 b4471 b0261 b0507 b2406 b2975 b0114 b3603 b2366 b0529 b2492 b0904 b3035 b2578 b1533 b3927 b3821 b2413 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.709227 (mmol/gDw/h)
  Minimum Production Rate : 0.001975 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.263522
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.110034
  EX_pi_e : 0.684124
  EX_so4_e : 0.626274
  EX_k_e : 0.138436
  EX_fe2_e : 0.011391
  EX_mg2_e : 0.006153
  EX_ca2_e : 0.003692
  EX_cl_e : 0.003692
  EX_cu2_e : 0.000503
  EX_mn2_e : 0.000490
  EX_zn2_e : 0.000242
  EX_ni2_e : 0.000229
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 46.530720
  EX_co2_e : 26.895186
  EX_h_e : 6.937073
  EX_ac_e : 0.860579
  EX_met__L_e : 0.447677
  DM_oxam_c : 0.002769
  DM_5drib_c : 0.002451
  DM_4crsol_c : 0.002133
  Auxiliary production reaction : 0.001975

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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