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 : 5mthf_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (112 of 120: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 60
  Gene deletion: b3553 b3399 b1241 b0351 b4069 b2744 b3708 b2297 b2458 b2779 b2926 b2883 b0121 b3962 b1982 b4139 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b1033 b4374 b0675 b2361 b2291 b1415 b1014 b4014 b0261 b2976 b0822 b2799 b4388 b3709 b4381 b3161 b0112 b2789 b3127 b4265 b4064 b4464 b0114 b2366 b2492 b0904 b2954 b1533 b3821 b1380 b4042 b1473 b0594 b4266 b3662 b1985   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.300648 (mmol/gDw/h)
  Minimum Production Rate : 0.162023 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.179238
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.119098
  EX_so4_e : 0.813339
  EX_pi_e : 0.290007
  EX_k_e : 0.058684
  EX_fe2_e : 0.004829
  EX_mg2_e : 0.002608
  EX_ca2_e : 0.001565
  EX_cl_e : 0.001565
  EX_cu2_e : 0.000213
  EX_mn2_e : 0.000208
  EX_zn2_e : 0.000103
  EX_ni2_e : 0.000097

Product: (mmol/gDw/h)
  EX_h2o_e : 47.590929
  EX_co2_e : 35.259305
  EX_h_e : 5.813629
  EX_ac_e : 2.329706
  EX_met__L_e : 0.737630
  EX_dxylnt_e : 0.162224
  Auxiliary production reaction : 0.162023
  DM_oxam_c : 0.000336
  DM_5drib_c : 0.000202
  DM_4crsol_c : 0.000067

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.

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Last updated: 21-Sep-2023
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