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 (31 of 92: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3553 b1478 b1241 b4069 b2297 b2458 b1004 b3713 b1109 b0046 b3236 b1033 b3945 b1602 b3915 b0755 b3612 b2492 b0904 b1380 b2660 b0514 b1517 b0606 b0221 b2285 b1010 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.494758 (mmol/gDw/h)
  Minimum Production Rate : 0.436231 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.312551
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.343340
  EX_pi_e : 0.477246
  EX_so4_e : 0.124590
  EX_k_e : 0.096573
  EX_fe3_e : 0.007946
  EX_mg2_e : 0.004292
  EX_ca2_e : 0.002575
  EX_cl_e : 0.002575
  EX_cu2_e : 0.000351
  EX_mn2_e : 0.000342
  EX_zn2_e : 0.000169
  EX_ni2_e : 0.000160
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 50.431567
  EX_co2_e : 37.806591
  EX_h_e : 4.842017
  EX_12ppd__S_e : 0.436231
  EX_ac_e : 0.288041
  DM_mththf_c : 0.000222
  DM_5drib_c : 0.000111
  DM_4crsol_c : 0.000110

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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