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 : dpcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b4467 b4382 b1241 b0351 b4069 b4384 b3708 b3926 b2297 b2458 b3617 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1982 b2797 b3117 b1814 b4471 b0261 b1602 b2406 b3915 b0114 b2366 b0755 b3612 b2492 b0904 b1533 b3821 b1380 b2660 b1771 b4141 b1798 b3662 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.389405 (mmol/gDw/h)
  Minimum Production Rate : 0.029304 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.451717
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.644417
  EX_pi_e : 0.434230
  EX_so4_e : 0.127364
  EX_k_e : 0.076009
  EX_fe3_e : 0.006254
  EX_mg2_e : 0.003378
  EX_ca2_e : 0.002027
  EX_cl_e : 0.002027
  EX_cu2_e : 0.000276
  EX_mn2_e : 0.000269
  EX_zn2_e : 0.000133
  EX_ni2_e : 0.000126

Product: (mmol/gDw/h)
  EX_h2o_e : 51.510631
  EX_co2_e : 34.964247
  EX_h_e : 7.161933
  EX_his__L_e : 1.077335
  EX_etoh_e : 0.729003
  EX_ac_e : 0.256010
  Auxiliary production reaction : 0.029304
  EX_hxan_e : 0.000436
  DM_5drib_c : 0.000261
  DM_4crsol_c : 0.000087

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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