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 : trp__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (12 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b2836 b3553 b4382 b1241 b0351 b4069 b4384 b3708 b3752 b2297 b2458 b2407 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b1033 b0261 b0507 b3709 b2406 b3161 b0112 b0114 b1539 b2492 b0904 b3035 b1533 b1473 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.465834 (mmol/gDw/h)
  Minimum Production Rate : 1.393913 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.919997
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.819310
  EX_pi_e : 0.449346
  EX_so4_e : 0.117306
  EX_k_e : 0.090927
  EX_fe2_e : 0.007482
  EX_mg2_e : 0.004041
  EX_ca2_e : 0.002425
  EX_cl_e : 0.002425
  EX_cu2_e : 0.000330
  EX_mn2_e : 0.000322
  EX_zn2_e : 0.000159
  EX_ni2_e : 0.000150
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 44.063943
  EX_co2_e : 20.610219
  EX_h_e : 9.536297
  EX_ac_e : 2.466852
  Auxiliary production reaction : 1.393913
  DM_oxam_c : 0.000521
  DM_5drib_c : 0.000313
  EX_glyclt_e : 0.000312
  DM_4crsol_c : 0.000104

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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