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 : dhpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (97 of 115: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b3553 b3399 b4069 b2744 b2297 b2458 b2926 b0160 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b3908 b1656 b0937 b1982 b4139 b1033 b4374 b0675 b2361 b2291 b0261 b2799 b3945 b1602 b0507 b1727 b0114 b0529 b2492 b0904 b2954 b1380 b2660 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.431095 (mmol/gDw/h)
  Minimum Production Rate : 0.250246 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.540962
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.159202
  EX_pi_e : 0.415837
  EX_so4_e : 0.108558
  EX_k_e : 0.084147
  EX_mg2_e : 0.003740
  EX_fe2_e : 0.003558
  EX_fe3_e : 0.003366
  EX_ca2_e : 0.002244
  EX_cl_e : 0.002244
  EX_cu2_e : 0.000306
  EX_mn2_e : 0.000298
  EX_zn2_e : 0.000147
  EX_ni2_e : 0.000139
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 53.225683
  EX_co2_e : 37.988942
  EX_h_e : 5.969074
  EX_ac_e : 0.250978
  Auxiliary production reaction : 0.250246
  EX_etoh_e : 0.153897
  EX_hxan_e : 0.000482
  DM_5drib_c : 0.000289
  DM_4crsol_c : 0.000096

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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