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 : accoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (8 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b4384 b2744 b3708 b3008 b0871 b0030 b2407 b0121 b1982 b2797 b3117 b1814 b4471 b4374 b2361 b2291 b0261 b0411 b0114 b0886 b2366 b2492 b0904 b0591 b2578 b1533 b3927 b3821 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.766077 (mmol/gDw/h)
  Minimum Production Rate : 0.105505 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.387251
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.012098
  EX_pi_e : 1.055477
  EX_so4_e : 0.298418
  EX_k_e : 0.149533
  EX_fe2_e : 0.012304
  EX_mg2_e : 0.006646
  EX_ca2_e : 0.003987
  EX_cl_e : 0.003987
  EX_cu2_e : 0.000543
  EX_mn2_e : 0.000529
  EX_zn2_e : 0.000261
  EX_ni2_e : 0.000247
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.467816
  EX_co2_e : 26.127750
  EX_h_e : 7.355533
  Auxiliary production reaction : 0.105505
  DM_5drib_c : 0.000514
  DM_4crsol_c : 0.000171

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