Computational protocol: Biochemical and kinetic characterisation of a novel xylooligosaccharide-upregulated GH43 β-d-xylosidase/α-l-arabinofuranosidase (BXA43) from the probiotic Bifidobacterium animalis subsp. lactis BB-12

Similar protocols

Protocol publication

[…] Sequences were retrieved of the 92 annotated GH43 enzymes in the CAZy database (Cantarel et al. ) and their multiple sequence alignment (ClustalW2; Goujon et al. ) was visualised with ESPript (Gouet et al. ) and used to construct a phylogenetic tree (Dendroscope; Huson et al. ).A homology model of BXA43 was built (HHPred; Söding et al. ) with XynB3 from Geobacillus stearothermophilus T-6 66% similarity, 50% identity; PDB: 2EXH, (Brüx et al. ) as template. X4 from the complex with BsAXH-m2,3 from Bacillus subtilis subsp. subtilis str. 168 (PDB: 3C7G, Vandermarliere et al. ) was superimposed at subsites +1 through +4. […]

Pipeline specifications

Software tools Clustal W, ESPript, Dendroscope, HHPred
Databases CAZy
Applications Phylogenetics, Protein structure analysis
Organisms Bifidobacterium animalis, Escherichia coli, Geobacillus stearothermophilus