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 : fpram_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (42 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b4467 b3399 b3942 b1732 b1241 b0351 b4069 b2744 b3115 b1849 b2296 b2926 b3617 b3844 b1238 b1004 b3713 b1109 b0046 b3236 b2883 b2210 b1623 b3665 b0411 b1602 b4381 b3654 b3714 b3664 b1727 b0114 b0529 b2492 b0904 b1380 b2660 b1511 b3662 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.343608 (mmol/gDw/h)
  Minimum Production Rate : 0.507806 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.363409
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.854649
  EX_pi_e : 0.839252
  EX_so4_e : 0.086527
  EX_k_e : 0.067070
  EX_fe2_e : 0.005519
  EX_mg2_e : 0.002981
  EX_ca2_e : 0.001788
  EX_cl_e : 0.001788
  EX_cu2_e : 0.000244
  EX_mn2_e : 0.000237
  EX_zn2_e : 0.000117
  EX_ni2_e : 0.000111

Product: (mmol/gDw/h)
  EX_h2o_e : 49.165251
  EX_co2_e : 32.470770
  EX_h_e : 5.993157
  EX_thymd_e : 0.810147
  Auxiliary production reaction : 0.507806
  EX_12ppd__R_e : 0.286975
  EX_ac_e : 0.200044
  DM_mththf_c : 0.000154
  DM_5drib_c : 0.000077
  DM_4crsol_c : 0.000077

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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