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 : grdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (41 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3553 b3399 b4269 b0493 b3588 b3003 b3011 b2066 b2744 b3926 b0871 b2925 b2097 b0160 b1004 b3713 b1109 b0046 b3236 b2690 b1033 b2361 b2291 b3945 b1602 b0114 b2492 b0904 b1380 b2660 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.412274 (mmol/gDw/h)
  Minimum Production Rate : 0.166074 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.432432
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.452528
  EX_pi_e : 0.729831
  EX_so4_e : 0.103819
  EX_k_e : 0.080473
  EX_fe2_e : 0.006622
  EX_mg2_e : 0.003576
  EX_cl_e : 0.002146
  EX_ca2_e : 0.002146
  EX_cu2_e : 0.000292
  EX_mn2_e : 0.000285
  EX_zn2_e : 0.000141
  EX_ni2_e : 0.000133
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 44.449931
  EX_co2_e : 28.888379
  EX_h_e : 7.798370
  EX_pyr_e : 4.176303
  Auxiliary production reaction : 0.166074
  DM_5drib_c : 0.000093
  DM_4crsol_c : 0.000092

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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