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 : trp__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b2836 b3553 b3399 b1241 b0351 b4069 b2502 b2744 b3708 b0871 b3115 b1849 b2296 b2925 b2097 b2690 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b1033 b4374 b0675 b2361 b2291 b0261 b3945 b3709 b3161 b0112 b0114 b0509 b3125 b1539 b2492 b0904 b3035 b1533 b1473 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.357820 (mmol/gDw/h)
  Minimum Production Rate : 1.070706 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.680845
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.006241
  EX_pi_e : 0.345156
  EX_so4_e : 0.090106
  EX_k_e : 0.069844
  EX_fe2_e : 0.005747
  EX_mg2_e : 0.003104
  EX_ca2_e : 0.001862
  EX_cl_e : 0.001862
  EX_cu2_e : 0.000254
  EX_mn2_e : 0.000247
  EX_zn2_e : 0.000122
  EX_ni2_e : 0.000116

Product: (mmol/gDw/h)
  EX_h2o_e : 44.747527
  EX_co2_e : 25.226273
  EX_h_e : 8.830870
  EX_ac_e : 1.894861
  EX_pyr_e : 1.505761
  Auxiliary production reaction : 1.070706
  DM_oxam_c : 0.000400
  DM_5drib_c : 0.000240
  EX_glyclt_e : 0.000239
  DM_4crsol_c : 0.000080

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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