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 (73 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b2836 b3553 b3399 b4382 b4069 b2744 b3708 b3008 b3115 b1849 b2296 b2779 b2925 b2097 b0160 b2690 b1982 b2797 b3117 b1814 b4471 b1033 b0675 b2361 b0261 b3945 b3709 b4381 b2406 b3161 b0112 b0114 b0886 b0509 b3125 b2366 b0529 b2492 b0904 b3035 b2578 b1533 b3927 b1473 b0515 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.577909 (mmol/gDw/h)
  Minimum Production Rate : 0.688897 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.671510
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.371128
  EX_pi_e : 1.935249
  EX_so4_e : 0.145529
  EX_k_e : 0.112804
  EX_mg2_e : 0.005013
  EX_fe2_e : 0.004769
  EX_fe3_e : 0.004512
  EX_cl_e : 0.003008
  EX_ca2_e : 0.003008
  EX_cu2_e : 0.000410
  EX_mn2_e : 0.000399
  EX_zn2_e : 0.000197
  EX_ni2_e : 0.000187
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 48.738998
  EX_co2_e : 27.169834
  EX_h_e : 8.178053
  EX_ac_e : 1.422618
  Auxiliary production reaction : 0.688897
  EX_alltn_e : 0.015768
  DM_5drib_c : 0.000388
  DM_4crsol_c : 0.000129

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