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 : adpglc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b4467 b2836 b1478 b3399 b1241 b4069 b2502 b2744 b3708 b3115 b1849 b2296 b2926 b1004 b3713 b1109 b0046 b3236 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0261 b2799 b3945 b1602 b2913 b2223 b3915 b2366 b2492 b0904 b1533 b1380 b4141 b1798 b0606 b2285 b1007 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.424945 (mmol/gDw/h)
  Minimum Production Rate : 0.354160 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.587920
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.362438
  EX_pi_e : 1.118179
  EX_so4_e : 0.107011
  EX_k_e : 0.082946
  EX_fe3_e : 0.006827
  EX_mg2_e : 0.003686
  EX_ca2_e : 0.002212
  EX_cl_e : 0.002212
  EX_cu2_e : 0.000301
  EX_mn2_e : 0.000294
  EX_zn2_e : 0.000145
  EX_ni2_e : 0.000137
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 51.529732
  EX_co2_e : 35.348836
  EX_h_e : 5.745977
  EX_glyclt_e : 0.522395
  Auxiliary production reaction : 0.354137
  EX_ac_e : 0.247398
  EX_ade_e : 0.000476
  DM_5drib_c : 0.000285
  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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