Based on this, a sketch map of the 3D-motif C in mVAChT (mouse VAChT) could be postulated on the basis of multiple sequence alignment and homology modelling (Fig. 5D).
On the basis of multiple sequence alignment and homology modeling, invariable structural elements were defined, corresponding to the active site, the substrate binding site, the accessory binding sites, the Ca2+ and Cl− binding sites, a protease-like catalytic triad and disulfide bonds.
Secondary structure prediction was performed with SOPMA (http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_sopma.html) on the basis of multiple sequence alignments [76].
While ConSurf calculates conservation scores on the basis of multiple sequence alignment typically of hundreds of homologous protein sequences, ProBiS usually uses tens of locally similar structures.
Since canine DNA sequence information on tenascinC, YKL39 and YKL40 was not available from public databases, degenerated primers were designed on the basis of multiple sequence alignment.
These primers were designed on the basis of multiple sequence alignment of the 2 known rabbit strains of HEV from China (3, 4 ) and 75 other genotype 3 HEV strains.
The first and the second sets of degenerative primers were designed on the basis of multiple sequence alignments derived from the helicase gene in open reading frame (ORF) 1 and the capsid gene in ORF2 (5 ), respectively.
On the basis of multiple sequence alignments to rooted phylogenic tree with branch length (UPGMA) of 16S rDNA sequence by CLUSTALW, the strain BI19 exhibited high level (99%) of similarity with the known sequences in the public databases in NCBI and BLAST results and identified as Bacillus subtilis (accession number FJ527663).
A bootstrapped NJ-tree was generated on basis of a multiple sequence alignment of all LacI-family TF homologs of L. plantarum, together with orthologous sequences for which experimental confirmation about the nature of the inducer could be retrieved.
