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 : fpram_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (21 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b1241 b0351 b4069 b2502 b2744 b3115 b1849 b2296 b2779 b0517 b1779 b1982 b3616 b3589 b4374 b0675 b2361 b2291 b0261 b4388 b0112 b0114 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.423094 (mmol/gDw/h)
  Minimum Production Rate : 1.621695 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.570001
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.436355
  EX_pi_e : 2.029814
  EX_so4_e : 0.106543
  EX_k_e : 0.082585
  EX_fe2_e : 0.006795
  EX_mg2_e : 0.003670
  EX_cl_e : 0.002202
  EX_ca2_e : 0.002202
  EX_cu2_e : 0.000300
  EX_mn2_e : 0.000292
  EX_zn2_e : 0.000144
  EX_ni2_e : 0.000137
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 44.756018
  EX_co2_e : 23.849799
  EX_h_e : 10.036642
  EX_ac_e : 2.903663
  Auxiliary production reaction : 1.621695
  EX_alltn_e : 0.000473
  DM_5drib_c : 0.000284
  EX_glyc__R_e : 0.000142
  DM_4crsol_c : 0.000094

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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