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 : prlp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 71: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4467 b4069 b4384 b2744 b3752 b3115 b1849 b2296 b2926 b2407 b1004 b3713 b1109 b0046 b3236 b1982 b4374 b2361 b2291 b0261 b2799 b3945 b1602 b2913 b2406 b3915 b1727 b0114 b0529 b2492 b0904 b1380 b3662 b0606 b2285 b1010 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.462674 (mmol/gDw/h)
  Minimum Production Rate : 0.216532 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.745239
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.082089
  EX_pi_e : 0.879362
  EX_so4_e : 0.116511
  EX_k_e : 0.090311
  EX_fe3_e : 0.007431
  EX_mg2_e : 0.004014
  EX_ca2_e : 0.002408
  EX_cl_e : 0.002408
  EX_cu2_e : 0.000328
  EX_mn2_e : 0.000320
  EX_zn2_e : 0.000158
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.226251
  EX_co2_e : 37.200965
  EX_h_e : 5.613275
  EX_ac_e : 0.269362
  Auxiliary production reaction : 0.216532
  EX_etoh_e : 0.009033
  EX_ade_e : 0.000518
  DM_5drib_c : 0.000310
  DM_4crsol_c : 0.000103

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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