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 : histd_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3553 b3831 b4069 b4384 b3708 b3008 b3115 b1849 b2296 b2779 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b1033 b0261 b1701 b1805 b0507 b4381 b2406 b0112 b0114 b2366 b0529 b2492 b0904 b2947 b2578 b1533 b3927 b0594 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.456102 (mmol/gDw/h)
  Minimum Production Rate : 0.579610 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 36.295687
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.665200
  EX_pi_e : 0.439958
  EX_so4_e : 0.114856
  EX_k_e : 0.089028
  EX_fe2_e : 0.007325
  EX_mg2_e : 0.003957
  EX_ca2_e : 0.002374
  EX_cl_e : 0.002374
  EX_cu2_e : 0.000323
  EX_mn2_e : 0.000315
  EX_zn2_e : 0.000156
  EX_ni2_e : 0.000147
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.211808
  EX_co2_e : 37.268354
  EX_h_e : 5.616621
  Auxiliary production reaction : 0.579610
  EX_ac_e : 0.265536
  DM_oxam_c : 0.000510
  DM_5drib_c : 0.000306
  DM_4crsol_c : 0.000102

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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