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 : 14dhncoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (29 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b2836 b3553 b3399 b1241 b0351 b4069 b2744 b3708 b2297 b2458 b3617 b0160 b3844 b0583 b1982 b2797 b3117 b1814 b4471 b1033 b4374 b0675 b2361 b2291 b4014 b0261 b2976 b0507 b3709 b3161 b0112 b0114 b2366 b2492 b0904 b1533 b1473 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.390542 (mmol/gDw/h)
  Minimum Production Rate : 0.584309 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.547990
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.308413
  EX_pi_e : 2.129645
  EX_so4_e : 0.682655
  EX_k_e : 0.076231
  EX_fe2_e : 0.006272
  EX_mg2_e : 0.003388
  EX_cl_e : 0.002033
  EX_ca2_e : 0.002033
  EX_cu2_e : 0.000277
  EX_mn2_e : 0.000270
  EX_zn2_e : 0.000133
  EX_ni2_e : 0.000126

Product: (mmol/gDw/h)
  EX_h2o_e : 46.055355
  EX_co2_e : 19.965024
  EX_h_e : 7.994960
  EX_ac_e : 2.652447
  Auxiliary production reaction : 0.584309
  DM_oxam_c : 0.000437
  DM_5drib_c : 0.000262
  EX_glyclt_e : 0.000261
  DM_4crsol_c : 0.000087

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