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 : dutp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b3399 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b3708 b3008 b0871 b2779 b2925 b2097 b3617 b2407 b2797 b3117 b1814 b4471 b3946 b0825 b3665 b0675 b2361 b2406 b0112 b3654 b3714 b3664 b0114 b2366 b2492 b0904 b1533 b1511 b1813 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.316411 (mmol/gDw/h)
  Minimum Production Rate : 0.763462 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.901767
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.944136
  EX_pi_e : 2.595598
  EX_so4_e : 0.079679
  EX_k_e : 0.061761
  EX_fe2_e : 0.005082
  EX_mg2_e : 0.002745
  EX_ca2_e : 0.001647
  EX_cl_e : 0.001647
  EX_cu2_e : 0.000224
  EX_mn2_e : 0.000219
  EX_zn2_e : 0.000108
  EX_ni2_e : 0.000102

Product: (mmol/gDw/h)
  EX_h2o_e : 46.305601
  EX_co2_e : 27.092220
  EX_h_e : 6.894100
  EX_pyr_e : 3.986683
  Auxiliary production reaction : 0.763462
  EX_acald_e : 0.544164
  DM_mththf_c : 0.000142
  EX_glyc__R_e : 0.000106
  DM_5drib_c : 0.000071
  DM_4crsol_c : 0.000071

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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