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 : dutp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4069 b4384 b3708 b3008 b3752 b0871 b2297 b2458 b2779 b2925 b2097 b2407 b1238 b0583 b2690 b2797 b3117 b1814 b4471 b3665 b3945 b2913 b4381 b2406 b0112 b3654 b3714 b3664 b0114 b0529 b1539 b2492 b0904 b2578 b1533 b3927 b3821 b3662 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.578728 (mmol/gDw/h)
  Minimum Production Rate : 0.737645 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.990351
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.725499
  EX_pi_e : 2.771178
  EX_so4_e : 0.145735
  EX_k_e : 0.112964
  EX_fe2_e : 0.009295
  EX_mg2_e : 0.005020
  EX_ca2_e : 0.003012
  EX_cl_e : 0.003012
  EX_cu2_e : 0.000410
  EX_mn2_e : 0.000400
  EX_zn2_e : 0.000197
  EX_ni2_e : 0.000187
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 48.897964
  EX_co2_e : 25.998880
  EX_h_e : 6.632193
  EX_pyr_e : 0.977686
  Auxiliary production reaction : 0.737645
  EX_ac_e : 0.336927
  DM_mththf_c : 0.000259
  DM_5drib_c : 0.000130
  DM_4crsol_c : 0.000129

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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