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 : 25aics_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 51
  Gene deletion: b3553 b1478 b3399 b4269 b0493 b3588 b3003 b3011 b1241 b2502 b2744 b0871 b1004 b3713 b1109 b0046 b3124 b3236 b1638 b1982 b4139 b1033 b4374 b0675 b2361 b2291 b4014 b0261 b2976 b2799 b3945 b1602 b2789 b3127 b3915 b0755 b3612 b0529 b2492 b0904 b2954 b1298 b3029 b1380 b1600 b2660 b0514 b1695 b1985 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.415580 (mmol/gDw/h)
  Minimum Production Rate : 0.459488 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.415561
  EX_o2_e : 287.456770
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.328502
  EX_pi_e : 0.860358
  EX_so4_e : 0.104652
  EX_k_e : 0.081118
  EX_mg2_e : 0.003605
  EX_ca2_e : 0.002163
  EX_cl_e : 0.002163
  EX_cu2_e : 0.000295
  EX_mn2_e : 0.000287
  EX_zn2_e : 0.000142
  EX_ni2_e : 0.000134
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993324
  EX_h2o_e : 552.995755
  EX_co2_e : 36.965766
  Auxiliary production reaction : 0.459487
  EX_ade_e : 0.000465
  DM_5drib_c : 0.000279
  DM_4crsol_c : 0.000093

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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