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 : dudp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (37 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b1478 b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b3831 b2744 b0512 b0871 b2925 b2097 b3617 b0160 b1779 b2690 b1982 b0675 b2361 b0822 b2913 b4381 b0112 b0511 b0114 b0529 b2492 b0904 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.316810 (mmol/gDw/h)
  Minimum Production Rate : 1.013718 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 36.233799
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.482964
  EX_pi_e : 2.333032
  EX_so4_e : 0.079779
  EX_k_e : 0.061839
  EX_fe2_e : 0.005088
  EX_mg2_e : 0.002748
  EX_ca2_e : 0.001649
  EX_cl_e : 0.001649
  EX_cu2_e : 0.000225
  EX_mn2_e : 0.000219
  EX_zn2_e : 0.000108
  EX_ni2_e : 0.000102

Product: (mmol/gDw/h)
  EX_h2o_e : 52.814801
  EX_co2_e : 36.262469
  EX_h_e : 3.958702
  Auxiliary production reaction : 1.013718
  EX_acald_e : 0.783635
  EX_xan_e : 0.008503
  DM_mththf_c : 0.000142
  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
Contact