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 : dump_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (31 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3752 b0871 b2297 b2458 b2925 b2097 b2926 b3617 b2407 b2690 b1982 b3665 b3945 b2406 b0112 b0114 b0529 b2492 b0904 b1511 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.297501 (mmol/gDw/h)
  Minimum Production Rate : 1.140705 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.839767
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.495400
  EX_pi_e : 1.427677
  EX_so4_e : 0.074917
  EX_k_e : 0.058070
  EX_fe2_e : 0.004778
  EX_mg2_e : 0.002581
  EX_ca2_e : 0.001548
  EX_cl_e : 0.001548
  EX_cu2_e : 0.000211
  EX_mn2_e : 0.000206
  EX_zn2_e : 0.000101
  EX_ni2_e : 0.000096

Product: (mmol/gDw/h)
  EX_h2o_e : 45.840069
  EX_co2_e : 26.669927
  EX_h_e : 8.777962
  EX_pyr_e : 3.327016
  Auxiliary production reaction : 1.140705
  EX_ac_e : 0.434974
  EX_ade_e : 0.000200
  DM_mththf_c : 0.000133
  DM_5drib_c : 0.000067
  DM_4crsol_c : 0.000066

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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