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 : prbatp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (42 of 47: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b4467 b4382 b3942 b1732 b4069 b4384 b3708 b3115 b1849 b2296 b0030 b2407 b1004 b3713 b1109 b0046 b1982 b2797 b3117 b1814 b4471 b2210 b0261 b1602 b2406 b0452 b1727 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b1380 b3662 b0606 b0221 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.468646 (mmol/gDw/h)
  Minimum Production Rate : 0.198517 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.734951
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.053917
  EX_pi_e : 1.246126
  EX_so4_e : 0.118014
  EX_k_e : 0.091476
  EX_mg2_e : 0.004065
  EX_fe2_e : 0.003868
  EX_fe3_e : 0.003659
  EX_ca2_e : 0.002439
  EX_cl_e : 0.002439
  EX_cu2_e : 0.000332
  EX_mn2_e : 0.000324
  EX_zn2_e : 0.000160
  EX_ni2_e : 0.000151
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.789852
  EX_co2_e : 37.239777
  EX_h_e : 5.178151
  EX_ac_e : 0.272839
  Auxiliary production reaction : 0.198517
  DM_5drib_c : 0.000314
  DM_4crsol_c : 0.000105

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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