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 : xmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (49 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4384 b2744 b3708 b3008 b0871 b0030 b2407 b1982 b2688 b2797 b3117 b1814 b4471 b2440 b3665 b4381 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b2240 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.779727 (mmol/gDw/h)
  Minimum Production Rate : 0.179439 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.102655
  EX_o2_e : 275.069576
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.141364
  EX_pi_e : 0.931568
  EX_so4_e : 0.196351
  EX_k_e : 0.152197
  EX_mg2_e : 0.006764
  EX_cl_e : 0.004058
  EX_ca2_e : 0.004058
  EX_cu2_e : 0.000553
  EX_mn2_e : 0.000539
  EX_zn2_e : 0.000266
  EX_ni2_e : 0.000252
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_fe3_e : 999.987477
  EX_h2o_e : 548.760279
  EX_co2_e : 26.197031
  Auxiliary production reaction : 0.179439
  EX_ade_e : 0.000525
  DM_mththf_c : 0.000349
  DM_5drib_c : 0.000175
  DM_4crsol_c : 0.000174

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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