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 : hemeO_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 98: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b0945 b3553 b1478 b1241 b0351 b3831 b4069 b4384 b3752 b3115 b1849 b2296 b2926 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b4139 b2498 b1033 b1623 b0261 b0411 b2799 b3945 b1602 b0507 b2913 b3915 b0529 b2492 b0904 b2954 b1380 b0723 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.325805 (mmol/gDw/h)
  Minimum Production Rate : 0.024913 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.473578
  EX_o2_e : 283.621823
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.416693
  EX_pi_e : 0.314274
  EX_so4_e : 0.082044
  EX_k_e : 0.063595
  EX_mg2_e : 0.002826
  EX_ca2_e : 0.001696
  EX_cl_e : 0.001696
  EX_cu2_e : 0.000231
  EX_mn2_e : 0.000225
  EX_zn2_e : 0.000111
  EX_ni2_e : 0.000105

Product: (mmol/gDw/h)
  EX_fe3_e : 999.969854
  EX_h2o_e : 549.009034
  EX_co2_e : 32.173307
  EX_ac_e : 1.997164
  EX_succ_e : 0.753903
  EX_ura_e : 0.646160
  EX_xtsn_e : 0.313773
  EX_ade_e : 0.050191
  DM_5drib_c : 0.050045
  Auxiliary production reaction : 0.024913
  DM_4crsol_c : 0.000073

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