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 : fgam_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (86 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 52
  Gene deletion: b1478 b3942 b1732 b0474 b2518 b1241 b0351 b4069 b4384 b2744 b1479 b3752 b3115 b1849 b2296 b2779 b3617 b2407 b3236 b2463 b3962 b1982 b0104 b2210 b4267 b1415 b3551 b1014 b0411 b3945 b2913 b4219 b1832 b1778 b4381 b0112 b2868 b0114 b0529 b1539 b2492 b0904 b1380 b0325 b1710 b2480 b0508 b4266 b3662 b1517 b0221 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.324020 (mmol/gDw/h)
  Minimum Production Rate : 0.979538 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.978445
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.116666
  EX_pi_e : 1.292089
  EX_so4_e : 0.081595
  EX_k_e : 0.063246
  EX_mg2_e : 0.002811
  EX_fe2_e : 0.002674
  EX_fe3_e : 0.002530
  EX_ca2_e : 0.001687
  EX_cl_e : 0.001687
  EX_cu2_e : 0.000230
  EX_mn2_e : 0.000224
  EX_zn2_e : 0.000110
  EX_ni2_e : 0.000105

Product: (mmol/gDw/h)
  EX_h2o_e : 48.131164
  EX_co2_e : 33.361865
  EX_h_e : 7.689842
  EX_ac_e : 2.092592
  Auxiliary production reaction : 0.979538
  EX_ade_e : 0.131641
  DM_mththf_c : 0.131424
  DM_5drib_c : 0.000217
  EX_dxylnt_e : 0.000217
  DM_4crsol_c : 0.000072

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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