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 (56 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b3553 b4382 b4069 b4384 b3708 b3008 b3752 b3115 b1849 b2296 b2407 b1982 b2797 b3117 b1814 b4471 b1033 b0595 b0261 b0507 b2342 b3845 b3709 b2406 b3161 b0112 b0653 b4077 b2663 b0452 b0114 b1216 b1186 b0842 b0019 b2366 b2492 b0904 b2578 b1533 b3927 b1473 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.695040 (mmol/gDw/h)
  Minimum Production Rate : 0.219004 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.454144
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.047415
  EX_pi_e : 1.327452
  EX_so4_e : 0.397647
  EX_k_e : 0.135667
  EX_fe2_e : 0.011163
  EX_mg2_e : 0.006029
  EX_ca2_e : 0.003618
  EX_cl_e : 0.003618
  EX_cu2_e : 0.000493
  EX_mn2_e : 0.000480
  EX_zn2_e : 0.000237
  EX_ni2_e : 0.000224
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 47.909176
  EX_co2_e : 25.158984
  EX_h_e : 7.672137
  EX_ac_e : 0.627264
  Auxiliary production reaction : 0.219004
  EX_cgly_e : 0.003618
  DM_oxam_c : 0.000778
  DM_5drib_c : 0.000466
  DM_4crsol_c : 0.000155

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