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 : damp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b1241 b0351 b4384 b3752 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b3617 b2407 b2690 b1982 b3945 b0114 b0755 b3612 b0529 b2492 b0904 b1518 b1813   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.669549 (mmol/gDw/h)
  Minimum Production Rate : 0.397075 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.165175
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.216903
  EX_pi_e : 1.042927
  EX_so4_e : 0.168606
  EX_k_e : 0.130691
  EX_fe2_e : 0.010754
  EX_mg2_e : 0.005808
  EX_ca2_e : 0.003485
  EX_cl_e : 0.003485
  EX_cu2_e : 0.000475
  EX_mn2_e : 0.000463
  EX_zn2_e : 0.000228
  EX_ni2_e : 0.000216
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 49.595080
  EX_co2_e : 26.450032
  EX_h_e : 8.836661
  EX_pyr_e : 0.698297
  Auxiliary production reaction : 0.397075
  DM_oxam_c : 0.000451
  DM_mththf_c : 0.000300
  DM_5drib_c : 0.000151
  DM_4crsol_c : 0.000149

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
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