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 : dudp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (50 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b4467 b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3752 b0871 b2407 b1004 b3713 b1109 b0046 b3236 b3616 b3589 b3665 b1602 b2913 b2406 b3654 b3714 b3664 b1727 b0114 b0529 b2492 b0904 b1380 b3662 b1518 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.379362 (mmol/gDw/h)
  Minimum Production Rate : 1.234233 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.958639
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.565539
  EX_pi_e : 2.834400
  EX_so4_e : 0.095531
  EX_k_e : 0.074049
  EX_mg2_e : 0.003291
  EX_fe2_e : 0.003131
  EX_fe3_e : 0.002962
  EX_ca2_e : 0.001975
  EX_cl_e : 0.001975
  EX_cu2_e : 0.000269
  EX_mn2_e : 0.000262
  EX_zn2_e : 0.000129
  EX_ni2_e : 0.000123

Product: (mmol/gDw/h)
  EX_h2o_e : 50.424985
  EX_co2_e : 31.463143
  EX_h_e : 4.722921
  Auxiliary production reaction : 1.234233
  EX_etoh_e : 0.928431
  DM_mththf_c : 0.000170
  DM_5drib_c : 0.000085
  DM_4crsol_c : 0.000085

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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