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 : 12ppd__S_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (50 of 92: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b1054 b3553 b1241 b0351 b0871 b2925 b2097 b2926 b3617 b1004 b3713 b1109 b0046 b3236 b3946 b0825 b1033 b1493 b3517 b4015 b3945 b1602 b2913 b2223 b1727 b1380 b0606 b2285 b3893 b1474 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.473352 (mmol/gDw/h)
  Minimum Production Rate : 0.384140 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.623313
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.112158
  EX_pi_e : 0.456598
  EX_so4_e : 0.119199
  EX_k_e : 0.092395
  EX_fe3_e : 0.007603
  EX_mg2_e : 0.004106
  EX_ca2_e : 0.002464
  EX_cl_e : 0.002464
  EX_cu2_e : 0.000336
  EX_mn2_e : 0.000327
  EX_zn2_e : 0.000161
  EX_ni2_e : 0.000153
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 45.094731
  EX_co2_e : 33.770244
  EX_h_e : 8.430411
  EX_for_e : 4.073465
  EX_etoh_e : 0.787480
  EX_12ppd__S_e : 0.384140
  DM_5drib_c : 0.000107
  DM_4crsol_c : 0.000106

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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