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 : hpyr_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3553 b1478 b3399 b1241 b0351 b4069 b2744 b2297 b2458 b2926 b0160 b1004 b3713 b1109 b0046 b3236 b3616 b3589 b1033 b4374 b2361 b2291 b0261 b1602 b0114 b0509 b3125 b0529 b2492 b0904 b1380 b2660 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.422016 (mmol/gDw/h)
  Minimum Production Rate : 0.204308 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.683422
  EX_o2_e : 288.314823
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.958659
  EX_pi_e : 0.407079
  EX_so4_e : 0.106272
  EX_k_e : 0.082375
  EX_mg2_e : 0.003661
  EX_ca2_e : 0.002197
  EX_cl_e : 0.002197
  EX_cu2_e : 0.000299
  EX_mn2_e : 0.000292
  EX_zn2_e : 0.000144
  EX_ni2_e : 0.000136
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993222
  EX_h2o_e : 550.558457
  EX_co2_e : 38.411418
  EX_ac_e : 1.425997
  DM_oxam_c : 0.400921
  Auxiliary production reaction : 0.204308
  DM_5drib_c : 0.000095
  DM_4crsol_c : 0.000094

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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