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 : didp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3553 b1478 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b0871 b2779 b3617 b1004 b3713 b1109 b0046 b3236 b1033 b1602 b4381 b0511 b4064 b4464 b0114 b0529 b2492 b0904 b1380 b2660 b0516 b1517 b0221 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.425812 (mmol/gDw/h)
  Minimum Production Rate : 0.454167 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.850840
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.472549
  EX_pi_e : 1.319076
  EX_so4_e : 0.107228
  EX_k_e : 0.083116
  EX_fe2_e : 0.006839
  EX_mg2_e : 0.003694
  EX_ca2_e : 0.002216
  EX_cl_e : 0.002216
  EX_cu2_e : 0.000302
  EX_mn2_e : 0.000294
  EX_zn2_e : 0.000145
  EX_ni2_e : 0.000138
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 53.051439
  EX_co2_e : 36.242619
  EX_h_e : 5.332178
  EX_acald_e : 0.839984
  Auxiliary production reaction : 0.454167
  EX_ade_e : 0.011428
  DM_mththf_c : 0.000191
  DM_5drib_c : 0.000096
  DM_4crsol_c : 0.000095

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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