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 : amp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b3553 b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2502 b4384 b2744 b3752 b0512 b0871 b1004 b3713 b1109 b0046 b2883 b1982 b3616 b3589 b2210 b1033 b1623 b4374 b2361 b2291 b0411 b0114 b0529 b2492 b0904 b1380 b3662 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.444485 (mmol/gDw/h)
  Minimum Production Rate : 0.721319 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.602838
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.413937
  EX_pi_e : 1.150072
  EX_so4_e : 0.111930
  EX_k_e : 0.086760
  EX_fe2_e : 0.007139
  EX_mg2_e : 0.003856
  EX_ca2_e : 0.002314
  EX_cl_e : 0.002314
  EX_cu2_e : 0.000315
  EX_mn2_e : 0.000307
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.705499
  EX_co2_e : 32.299904
  EX_h_e : 7.697642
  EX_acald_e : 1.113860
  Auxiliary production reaction : 0.721319
  EX_alltn_e : 0.001735
  DM_mththf_c : 0.001437
  DM_5drib_c : 0.000298
  DM_4crsol_c : 0.000099

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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