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 : 14dhncoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (37 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b3553 b1241 b0351 b4069 b4384 b3708 b3752 b2297 b2458 b3617 b2407 b1238 b1982 b2797 b3117 b1814 b4471 b1033 b3665 b0261 b3709 b4381 b2406 b3161 b0112 b0114 b0509 b3125 b2366 b2492 b0904 b1533 b3821 b1473 b0594 b4141 b1798 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.317843 (mmol/gDw/h)
  Minimum Production Rate : 0.475553 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.487094
  EX_o2_e : 276.261844
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.763325
  EX_pi_e : 1.733253
  EX_so4_e : 0.555592
  EX_k_e : 0.062041
  EX_mg2_e : 0.002757
  EX_cl_e : 0.001654
  EX_ca2_e : 0.001654
  EX_cu2_e : 0.000225
  EX_mn2_e : 0.000220
  EX_zn2_e : 0.000108
  EX_ni2_e : 0.000103

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994895
  EX_h2o_e : 548.650320
  EX_co2_e : 27.416031
  EX_ac_e : 2.158685
  Auxiliary production reaction : 0.475553
  EX_ade_e : 0.000356
  DM_5drib_c : 0.000213
  EX_glyclt_e : 0.000213
  DM_4crsol_c : 0.000071

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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