Using sequence alignments of HIV proteins of different subtypes, we show that MAPK docking patterns previously described for human proteins appear on the HIV matrix, Tat, and Vif proteins in a strain dependent manner, but are absent from HIV Rev and appear on all HIV Nef strains.
The RNA secondary structure of sequences encoding selenoproteins was analyzed with the Centroid_alifold program (Hamada et al. 2009) using sequence alignments of the region around the TGA codon (−10; +60) of the formate dehydrogenase (Fdh), SelD, and SelW protein families.
Using sequence alignments of type I BVMOs and crystal structures of PAMO and cyclohexanone monooxygenase in complex with NADP+, we identified four residues that could interact with the 2′-phosphate moiety of NADPH in PAMO.
This uses sequence alignments of homologous proteins to predict amino acid substitutions likely to be tolerated without loss of function.
We used sequence alignments of these sequence pairs to compute substitutions of amino acids between mesophilic and psychrophilic proteomes and vice versa and the obtained values were averaged.
We used sequence alignments of ≈20 kb located upstream of the pbp2x gene of 2 serotype 8 (strainstrains (2071247 [GenBank accession no.
In this study, we have used sequence alignments of YLR106p and its orthologs from widely diverse eukaryotes to identify and characterize five major functional domains in the protein.
In order to evaluate the power of our identification method, simulations were performed using sequence alignment sets of random sequences, each consisting of 100,000 pairs of around 5,000 bp sequences and including an inversion in each pair.
Sequencing was performed using the BigDye terminator cycle sequencing method on an ABI Prism Genetic Analyzer Applied Biosystemss, Foster City, CA) and compared with the revised Cambridge reference sequence using sequence alignment software of the European Molecular Biology Open Software Suite EMBOSSS, http://www.ebi.ac.uk/emboss/align/).ac.uk/emboss/align/
Using sequence alignment analysis of known aquaporin genes from cotton and several other plants, conserved sequence regions were selected for use in designing degenerate primers in the forward and reverse direction (Additional file 1).
