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 : adn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (84 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b4467 b4382 b1241 b0351 b4384 b2930 b4232 b3697 b3925 b0871 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b2690 b3665 b0411 b2799 b3945 b1602 b0153 b2913 b0590 b3654 b3714 b3664 b1727 b0529 b1539 b2492 b0904 b3927 b1380 b1518 b0606 b2285 b1008   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.442651 (mmol/gDw/h)
  Minimum Production Rate : 0.017513 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.395529
  EX_o2_e : 284.088648
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.868161
  EX_pi_e : 0.426984
  EX_so4_e : 0.111468
  EX_k_e : 0.086402
  EX_mg2_e : 0.003840
  EX_ca2_e : 0.002304
  EX_cl_e : 0.002304
  EX_cu2_e : 0.000314
  EX_mn2_e : 0.000306
  EX_zn2_e : 0.000151
  EX_ni2_e : 0.000143
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992891
  EX_h2o_e : 544.648282
  EX_co2_e : 32.769999
  EX_glyclt_e : 4.442540
  Auxiliary production reaction : 0.017513
  DM_mththf_c : 0.000198
  DM_5drib_c : 0.000100
  DM_4crsol_c : 0.000099

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.

Last updated: 21-Sep-2023
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