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 : dmpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 111: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b1241 b0351 b4069 b4384 b2744 b2297 b2458 b2925 b2097 b0030 b2407 b1779 b2690 b1982 b3616 b3589 b4374 b2361 b2291 b3945 b0114 b0529 b2492 b0904 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.534012 (mmol/gDw/h)
  Minimum Production Rate : 0.069620 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.474053
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.756606
  EX_pi_e : 0.654350
  EX_so4_e : 0.134475
  EX_k_e : 0.104235
  EX_fe2_e : 0.008577
  EX_mg2_e : 0.004633
  EX_ca2_e : 0.002780
  EX_cl_e : 0.002780
  EX_cu2_e : 0.000379
  EX_mn2_e : 0.000369
  EX_zn2_e : 0.000182
  EX_ni2_e : 0.000172
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 43.488675
  EX_co2_e : 27.269013
  EX_h_e : 8.585486
  EX_ac_e : 1.769741
  DM_oxam_c : 0.989326
  DM_mththf_c : 0.988968
  Auxiliary production reaction : 0.069620
  DM_5drib_c : 0.000358
  DM_4crsol_c : 0.000119

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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