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 : 5mthf_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (23 of 120: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b3553 b4382 b4384 b3708 b3008 b3752 b0871 b2407 b0121 b1982 b2797 b3117 b1814 b4471 b1033 b2440 b0261 b3709 b2406 b3161 b0112 b0452 b0114 b0886 b0509 b3125 b1539 b2492 b0904 b0591 b2578 b1533 b3927 b1473 b4141 b1798 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.555075 (mmol/gDw/h)
  Minimum Production Rate : 0.127380 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.737548
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.887090
  EX_pi_e : 0.535429
  EX_so4_e : 0.139779
  EX_k_e : 0.108347
  EX_fe2_e : 0.008915
  EX_mg2_e : 0.004815
  EX_ca2_e : 0.002889
  EX_cl_e : 0.002889
  EX_cu2_e : 0.000394
  EX_mn2_e : 0.000384
  EX_zn2_e : 0.000189
  EX_ni2_e : 0.000179
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 51.618626
  EX_co2_e : 34.666545
  EX_h_e : 6.120533
  Auxiliary production reaction : 0.127380
  DM_oxam_c : 0.000621
  DM_5drib_c : 0.000372
  DM_4crsol_c : 0.000124
  EX_etha_e : 0.000045

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