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 : cdigmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (50 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b2836 b4384 b2744 b3708 b3008 b0871 b2926 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b0261 b0411 b4381 b0114 b2366 b0529 b2492 b0904 b2578 b1533 b3927 b2413 b3447 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.688939 (mmol/gDw/h)
  Minimum Production Rate : 0.079040 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.026365
  EX_o2_e : 279.140982
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.230886
  EX_pi_e : 0.822635
  EX_so4_e : 0.173489
  EX_k_e : 0.134476
  EX_mg2_e : 0.005977
  EX_ca2_e : 0.003586
  EX_cl_e : 0.003586
  EX_cu2_e : 0.000488
  EX_mn2_e : 0.000476
  EX_zn2_e : 0.000235
  EX_ni2_e : 0.000223
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988935
  EX_h2o_e : 550.382363
  EX_co2_e : 30.139871
  Auxiliary production reaction : 0.079040
  DM_5drib_c : 0.000462
  DM_4crsol_c : 0.000154

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