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 : idp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4467 b3399 b4069 b2502 b2744 b3115 b1849 b2296 b2779 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b4374 b0675 b2361 b2291 b3945 b1602 b2913 b3915 b1727 b0114 b0529 b2492 b0904 b1380 b1517 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.442835 (mmol/gDw/h)
  Minimum Production Rate : 0.204629 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.353669
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.602290
  EX_pi_e : 0.836419
  EX_so4_e : 0.111515
  EX_k_e : 0.086438
  EX_fe3_e : 0.007112
  EX_mg2_e : 0.003842
  EX_ca2_e : 0.002305
  EX_cl_e : 0.002305
  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_h2o_e : 51.936875
  EX_co2_e : 37.788149
  EX_h_e : 5.439318
  EX_3hpp_e : 0.490368
  EX_ac_e : 0.257812
  Auxiliary production reaction : 0.204629
  EX_hxan_e : 0.000298
  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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