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 : sbzcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (25 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b2836 b3553 b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2502 b2744 b3708 b3008 b0871 b3617 b0120 b1982 b2797 b3117 b1814 b4471 b1033 b4374 b0675 b2361 b2291 b0261 b0507 b0112 b0114 b0886 b2366 b2492 b0904 b3035 b2578 b1533 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.506967 (mmol/gDw/h)
  Minimum Production Rate : 0.407283 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.703036
  EX_o2_e : 270.447303
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.326790
  EX_pi_e : 1.710872
  EX_so4_e : 0.534947
  EX_k_e : 0.098956
  EX_mg2_e : 0.004398
  EX_ca2_e : 0.002639
  EX_cl_e : 0.002639
  EX_cu2_e : 0.000359
  EX_mn2_e : 0.000350
  EX_zn2_e : 0.000173
  EX_ni2_e : 0.000164
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991858
  EX_h2o_e : 546.755158
  EX_co2_e : 22.781140
  EX_acald_e : 1.687056
  Auxiliary production reaction : 0.407283
  DM_oxam_c : 0.000567
  DM_5drib_c : 0.000340
  EX_glyclt_e : 0.000339
  DM_4crsol_c : 0.000113
  EX_etha_e : 0.000041

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