The putative domains of irrE from D. radiodurans were determined by sequence alignment with irrE from D. deserti as described (see Figure 9).
Sequence alignments from Smith et al. (2009) were provided by Gavin Smith.
In the Pycnoporus a1-1 prothen, the position of the HD1 homeodomain is only recognized by sequence alignment with related HD1 proteins from other species (Additional file 20: Figure S5 A).
The secondary structures for the rrnL and rrnS were predicted by sequence alignment against rrnL and rrnS from Ne. americanus [ 32] with secondary structures for variable regions determined using MFOLD [ 55].
By sequence alignment analysis of TEX11 homologues from diverse species (human, mouse, rat, horse, cat, dog, marsupial, chicken, and fish), we found that three of these mutations affect residues that are highly evolutionary conserved and may therefore be important for functional and/or structural integrity (W117, Q172, and V748; Supplementary Fig S1).
While CBM1s from oomycetes share similarity with fungal CBM1s, they also display specific features, as revealed by sequence alignment and structural modeling of CBM1s from CBEL.
Contact: [email protected] Information retrieval from molecular databases by sequence alignment is an essential component of modern biology.
This can be done either by constructing a multiple sequence alignment from the best matching hits with subsequent phylogenetic reconstruction, as implemented in Phylogena [ 58], or it can be done directly based on the BLAST results.
Using a multiple sequence alignment from a study by Karol et al. (2001), which was slightly modified by Yang and Rannala (2005), the phylogeny of the small subunit rRNA gene (SSU rRNA) from the nuclear genome of eight land plants and six charales (see Fig. 3) has been reconstructed.
We examined the conservation of these motifs by multiple sequence alignments of DGs from species representative of the phyla identified in our phylogenetic survey.
