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 : dcdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (28 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3399 b2066 b1241 b0351 b4069 b2502 b2744 b3708 b0910 b2297 b2458 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b4374 b0675 b2361 b2291 b0261 b0112 b0114 b2366 b2492 b0904 b1533 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.429200 (mmol/gDw/h)
  Minimum Production Rate : 1.284328 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 29.214509
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.488783
  EX_pi_e : 2.982665
  EX_so4_e : 0.108081
  EX_k_e : 0.083777
  EX_fe2_e : 0.006893
  EX_mg2_e : 0.003723
  EX_ca2_e : 0.002234
  EX_cl_e : 0.002234
  EX_cu2_e : 0.000304
  EX_mn2_e : 0.000297
  EX_zn2_e : 0.000146
  EX_ni2_e : 0.000139
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 51.739363
  EX_co2_e : 28.845477
  EX_h_e : 7.501765
  Auxiliary production reaction : 1.284328
  EX_ac_e : 0.988492
  DM_oxam_c : 0.000480
  DM_5drib_c : 0.000288
  DM_4crsol_c : 0.000096

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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