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 : 6hmhptpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (45 of 95: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b4382 b1241 b0351 b4069 b2502 b4384 b2744 b2297 b2458 b3617 b1982 b0675 b2361 b2291 b0261 b0112 b2975 b0114 b3603 b0509 b3125 b0529 b2492 b0904 b0508   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.512520 (mmol/gDw/h)
  Minimum Production Rate : 0.504307 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.130485
  EX_nh4_e : 10.977600
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.502995
  EX_so4_e : 0.129063
  EX_k_e : 0.100040
  EX_fe2_e : 0.008232
  EX_mg2_e : 0.004446
  EX_ca2_e : 0.002668
  EX_cl_e : 0.002668
  EX_cu2_e : 0.000363
  EX_mn2_e : 0.000354
  EX_zn2_e : 0.000175
  EX_ni2_e : 0.000166
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 48.580643
  EX_co2_e : 20.232622
  EX_h_e : 9.946314
  EX_thymd_e : 1.460156
  Auxiliary production reaction : 0.504307
  EX_ac_e : 0.298382
  DM_oxam_c : 0.000574
  DM_5drib_c : 0.000344
  DM_4crsol_c : 0.000114

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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