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 : 14dhncoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (40 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b3399 b4069 b2502 b2744 b3708 b3008 b2297 b2458 b0583 b2797 b3117 b1814 b4471 b1623 b3665 b4374 b0675 b2361 b2291 b0411 b3709 b3161 b0112 b3654 b3714 b3664 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b3825 b1473 b0494 b4141 b1798 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.671141 (mmol/gDw/h)
  Minimum Production Rate : 0.213858 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 22.752521
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.745272
  EX_pi_e : 1.288962
  EX_so4_e : 0.382865
  EX_k_e : 0.131002
  EX_fe2_e : 0.010779
  EX_mg2_e : 0.005822
  EX_ca2_e : 0.003493
  EX_cl_e : 0.003493
  EX_cu2_e : 0.000476
  EX_mn2_e : 0.000464
  EX_zn2_e : 0.000229
  EX_ni2_e : 0.000217
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 47.895757
  EX_co2_e : 24.398608
  EX_h_e : 7.412871
  EX_ac_e : 0.604587
  Auxiliary production reaction : 0.213858
  DM_mththf_c : 0.000301
  DM_5drib_c : 0.000151
  DM_4crsol_c : 0.000150

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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