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 : trp__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (1 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4382 b4384 b3708 b3008 b3752 b0871 b2407 b0120 b1982 b2797 b3117 b1814 b4471 b0261 b0507 b3709 b2406 b3161 b0112 b0114 b0886 b1539 b2492 b0904 b0591 b2578 b1533 b3927 b3821 b1473 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.761423 (mmol/gDw/h)
  Minimum Production Rate : 0.258979 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.107719
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.744232
  EX_pi_e : 0.734473
  EX_so4_e : 0.191741
  EX_k_e : 0.148624
  EX_fe2_e : 0.012229
  EX_mg2_e : 0.006605
  EX_ca2_e : 0.003963
  EX_cl_e : 0.003963
  EX_cu2_e : 0.000540
  EX_mn2_e : 0.000526
  EX_zn2_e : 0.000260
  EX_ni2_e : 0.000246
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.052202
  EX_co2_e : 25.860992
  EX_h_e : 7.522280
  Auxiliary production reaction : 0.258979
  DM_oxam_c : 0.002973
  DM_5drib_c : 0.002631
  DM_4crsol_c : 0.002290
  EX_glyclt_e : 0.002121

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