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 : gsn_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (41 of 49: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3399 b4382 b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b0871 b2407 b3236 b1982 b3616 b3589 b2210 b0675 b2361 b0112 b0114 b0755 b3612 b0529 b2492 b0904 b0515 b1518 b1813   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.554086 (mmol/gDw/h)
  Minimum Production Rate : 0.899182 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.296838
  EX_nh4_e : 10.488645
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.534475
  EX_so4_e : 0.139530
  EX_k_e : 0.108154
  EX_fe2_e : 0.008899
  EX_mg2_e : 0.004807
  EX_cl_e : 0.002884
  EX_ca2_e : 0.002884
  EX_cu2_e : 0.000393
  EX_mn2_e : 0.000383
  EX_zn2_e : 0.000189
  EX_ni2_e : 0.000179
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 50.007640
  EX_co2_e : 25.469616
  EX_h_e : 9.595726
  EX_acald_e : 1.388516
  EX_gsn_e : 0.899182
  EX_alltn_e : 0.002163
  DM_mththf_c : 0.001791
  DM_5drib_c : 0.000372
  DM_4crsol_c : 0.000124

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